1
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Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
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Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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2
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He Y, Zhu G, Li X, Zhou M, Guan MX. Deficient tRNA posttranscription modification dysregulated the mitochondrial quality controls and apoptosis. iScience 2024; 27:108883. [PMID: 38318358 PMCID: PMC10838789 DOI: 10.1016/j.isci.2024.108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Mitochondria are dynamic organelles in cellular metabolism and physiology. Mitochondrial DNA (mtDNA) mutations are associated with a broad spectrum of clinical abnormalities. However, mechanisms underlying mtDNA mutations regulate intracellular signaling related to the mitochondrial and cellular integrity are less explored. Here, we demonstrated that mt-tRNAMet 4435A>G mutation-induced nucleotide modification deficiency dysregulated the expression of nuclear genes involved in cytosolic proteins involved in oxidative phosphorylation system (OXPHOS) and impaired the assemble and integrity of OXPHOS complexes. These dysfunctions caused mitochondrial dynamic imbalance, thereby increasing fission and decreasing fusion. Excessive fission impaired the process of autophagy including initiation phase, formation, and maturation of autophagosome. Strikingly, the m.4435A>G mutation upregulated the PARKIN dependent mitophagy pathways but downregulated the ubiquitination-independent mitophagy. These alterations promoted intrinsic apoptotic process for the removal of damaged cells. Our findings provide new insights into mechanism underlying deficient tRNA posttranscription modification regulated intracellular signaling related to the mitochondrial and cellular integrity.
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Affiliation(s)
- Yunfan He
- Center for Mitochondrial Biomedicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Center for Genetic Medicine, Zhejiang University International Institute of Medicine, Yiwu, Zhejiang, China
| | - Gao Zhu
- Center for Mitochondrial Biomedicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Center for Genetic Medicine, Zhejiang University International Institute of Medicine, Yiwu, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Xincheng Li
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
| | - Mi Zhou
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
| | - Min-Xin Guan
- Center for Mitochondrial Biomedicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Center for Genetic Medicine, Zhejiang University International Institute of Medicine, Yiwu, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
- Key Lab of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang, China
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3
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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4
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Pyrih J, Hammond M, Alves A, Dean S, Sunter JD, Wheeler RJ, Gull K, Lukeš J. Comprehensive sub-mitochondrial protein map of the parasitic protist Trypanosoma brucei defines critical features of organellar biology. Cell Rep 2023; 42:113083. [PMID: 37669165 DOI: 10.1016/j.celrep.2023.113083] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/30/2023] [Accepted: 08/17/2023] [Indexed: 09/07/2023] Open
Abstract
We have generated a high-confidence mitochondrial proteome (MitoTag) of the Trypanosoma brucei procyclic stage containing 1,239 proteins. For 337 of these, a mitochondrial localization had not been described before. We use the TrypTag dataset as a foundation and take advantage of the properties of the fluorescent protein tag that causes aberrant but fortuitous accumulation of tagged matrix and inner membrane proteins near the kinetoplast (mitochondrial DNA). Combined with transmembrane domain predictions, this characteristic allowed categorization of 1,053 proteins into mitochondrial sub-compartments, the detection of unique matrix-localized fucose and methionine synthesis, and the identification of new kinetoplast proteins, which showed kinetoplast-linked pyrimidine synthesis. Moreover, disruption of targeting signals by tagging allowed mapping of the mode of protein targeting to these sub-compartments, identifying a set of C-tail anchored outer mitochondrial membrane proteins and mitochondrial carriers likely employing multiple target peptides. This dataset represents a comprehensive, updated mapping of the mitochondrion.
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Affiliation(s)
- Jan Pyrih
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Department of Biochemistry, University of Cambridge, Cambridge, UK; Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | | | - Samuel Dean
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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5
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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6
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Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
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7
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Paris Z, Svobodová M, Kachale A, Horáková E, Nenarokova A, Lukeš J. A mitochondrial cytidine deaminase is responsible for C to U editing of tRNA Trp to decode the UGA codon in Trypanosoma brucei. RNA Biol 2021; 18:278-286. [PMID: 34224320 PMCID: PMC8677022 DOI: 10.1080/15476286.2021.1940445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In kinetoplastid protists, all mitochondrial tRNAs are encoded in the nucleus and imported from the cytoplasm to maintain organellar translation. This also applies to the tryptophanyl tRNA (tRNATrp) encoded by a single-copy nuclear gene, with a CCA anticodon to read UGG codon used in the cytosolic translation. Yet, in the mitochondrion it is unable to decode the UGA codon specifying tryptophan. Following mitochondrial import of tRNATrp, this problem is solved at the RNA level by a single C34 to U34 editing event that creates the UCA anticodon, recognizing UGA. To identify the enzyme responsible for this critical editing activity, we scrutinized the genome of Trypanosoma brucei for putative cytidine deaminases as the most likely candidates. Using RNAi silencing and poisoned primer extension, we have identified a novel deaminase enzyme, named here TbmCDAT for mitochondrial Cytidine Deaminase Acting on tRNA, which is responsible for this organelle-specific activity in T. brucei. The ablation of TbmCDAT led to the downregulation of mitochondrial protein synthesis, supporting its role in decoding the UGA tryptophan codon.
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Affiliation(s)
- Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Michaela Svobodová
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
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8
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Guo Q, Ng PQ, Shi S, Fan D, Li J, Zhao J, Wang H, David R, Mittal P, Do T, Bock R, Zhao M, Zhou W, Searle I. Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth. PLoS One 2019; 14:e0225064. [PMID: 31756231 PMCID: PMC6874348 DOI: 10.1371/journal.pone.0225064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/28/2019] [Indexed: 12/30/2022] Open
Abstract
Modified nucleosides in tRNAs are critical for protein translation. N1-methylguanosine-37 and N1-methylinosine-37 in tRNAs, both located at the 3'-adjacent to the anticodon, are formed by Trm5. Here we describe Arabidopsis thaliana AtTRM5 (At3g56120) as a Trm5 ortholog. Attrm5 mutant plants have overall slower growth as observed by slower leaf initiation rate, delayed flowering and reduced primary root length. In Attrm5 mutants, mRNAs of flowering time genes are less abundant and correlated with delayed flowering. We show that AtTRM5 complements the yeast trm5 mutant, and in vitro methylates tRNA guanosine-37 to produce N1-methylguanosine (m1G). We also show in vitro that AtTRM5 methylates tRNA inosine-37 to produce N1-methylinosine (m1I) and in Attrm5 mutant plants, we show a reduction of both N1-methylguanosine and N1-methylinosine. We also show that AtTRM5 is localized to the nucleus in plant cells. Proteomics data showed that photosynthetic protein abundance is affected in Attrm5 mutant plants. Finally, we show tRNA-Ala aminoacylation is not affected in Attrm5 mutants. However the abundance of tRNA-Ala and tRNA-Asp 5' half cleavage products are deduced. Our findings highlight the bifunctionality of AtTRM5 and the importance of the post-transcriptional tRNA modifications m1G and m1I at tRNA position 37 in general plant growth and development.
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Affiliation(s)
- Qianqian Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pei Qin Ng
- School of Biological Sciences, School of Agriculture, Food and Wine, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, The University of Adelaide, Adelaide, Adelaide, Australia
| | - Shanshan Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diwen Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Li
- School of Biological Sciences, School of Agriculture, Food and Wine, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, The University of Adelaide, Adelaide, Adelaide, Australia
| | - Jing Zhao
- School of Biological Sciences, School of Agriculture, Food and Wine, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, The University of Adelaide, Adelaide, Adelaide, Australia
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Rakesh David
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Parul Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, The University of Adelaide, SA, Australia
| | - Trung Do
- School of Biological Sciences, School of Agriculture, Food and Wine, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, The University of Adelaide, Adelaide, Adelaide, Australia
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Ming Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Iain Searle
- School of Biological Sciences, School of Agriculture, Food and Wine, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, The University of Adelaide, Adelaide, Adelaide, Australia
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9
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Jin X, Lv Z, Gao J, Zhang R, Zheng T, Yin P, Li D, Peng L, Cao X, Qin Y, Persson S, Zheng B, Chen P. AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. Nucleic Acids Res 2019; 47:883-898. [PMID: 30508117 PMCID: PMC6344853 DOI: 10.1093/nar/gky1205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Modified nucleosides on tRNA are critical for decoding processes and protein translation. tRNAs can be modified through 1-methylguanosine (m1G) on position 37; a function mediated by Trm5 homologs. We show that AtTRM5a (At3g56120) is a Trm5 ortholog in Arabidopsis thaliana. AtTrm5a is localized to the nucleus and its function for m1G and m1I methylation was confirmed by mutant analysis, yeast complementation, m1G nucleoside level on single tRNA, and tRNA in vitro methylation. Arabidopsis attrm5a mutants were dwarfed and had short filaments, which led to reduced seed setting. Proteomics data indicated differences in the abundance of proteins involved in photosynthesis, ribosome biogenesis, oxidative phosphorylation and calcium signalling. Levels of phytohormone auxin and jasmonate were reduced in attrm5a mutant, as well as expression levels of genes involved in flowering, shoot apex cell fate determination, and hormone synthesis and signalling. Taken together, loss-of-function of AtTrm5a impaired m1G and m1I methylation and led to aberrant protein translation, disturbed hormone homeostasis and developmental defects in Arabidopsis plants.
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Affiliation(s)
- Xiaohuan Jin
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Zhengyi Lv
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Junbao Gao
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Rui Zhang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Ting Zheng
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China.,National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China.,National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement, HuaZhong Agricultural University, Wuhan 430070, China
| | - Liangcai Peng
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xintao Cao
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Yan Qin
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville 3010, VIC, Australia.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, HuaZhong Agricultural University, Wuhan 430070, China
| | - Peng Chen
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China.,Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
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10
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Jacob D, Thüring K, Galliot A, Marchand V, Galvanin A, Ciftci A, Scharmann K, Stock M, Roignant J, Leidel SA, Motorin Y, Schaffrath R, Klassen R, Helm M. Absolute Quantification of Noncoding RNA by Microscale Thermophoresis. Angew Chem Int Ed Engl 2019; 58:9565-9569. [PMID: 30892798 PMCID: PMC6617968 DOI: 10.1002/anie.201814377] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 01/08/2023]
Abstract
Accurate quantification of the copy numbers of noncoding RNA has recently emerged as an urgent problem, with impact on fields such as RNA modification research, tissue differentiation, and others. Herein, we present a hybridization-based approach that uses microscale thermophoresis (MST) as a very fast and highly precise readout to quantify, for example, single tRNA species with a turnaround time of about one hour. We developed MST to quantify the effect of tRNA toxins and of heat stress and RNA modification on single tRNA species. A comparative analysis also revealed significant differences to RNA-Seq-based quantification approaches, strongly suggesting a bias due to tRNA modifications in the latter. Further applications include the quantification of rRNA as well as of polyA levels in cellular RNA.
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Affiliation(s)
- Dominik Jacob
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Kathrin Thüring
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Aurellia Galliot
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
| | - Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Akif Ciftci
- Institute for Biochemistry and Molecular BiologyFaculty of MedicineUniversity of FreiburgStefan-Meier-Str. 1779104FreiburgGermany
| | - Karin Scharmann
- Max Planck Research Group for RNA BiologyMax Planck Institute for Molecular BiomedicineVon-Esmarch-Str. 5448149MünsterGermany
| | - Michael Stock
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
| | | | - Sebastian A. Leidel
- Max Planck Research Group for RNA BiologyMax Planck Institute for Molecular BiomedicineVon-Esmarch-Str. 5448149MünsterGermany
| | - Yuri Motorin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL9, Avenue de la Forêt de Haye54505Vandoeuvre-les-NancyFrance
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet MikrobiologieUniversität KasselHeinrich-Plett-Str. 4034132KasselGermany
| | - Roland Klassen
- Institut für Biologie, Fachgebiet MikrobiologieUniversität KasselHeinrich-Plett-Str. 4034132KasselGermany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University MainzStaudingerweg 555128MainzGermany
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11
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Jacob D, Thüring K, Galliot A, Marchand V, Galvanin A, Ciftci A, Scharmann K, Stock M, Roignant J, Leidel SA, Motorin Y, Schaffrath R, Klassen R, Helm M. Absolute Quantifizierung nicht‐kodierender RNA‐Spezies mittels Mikroskala‐Thermophorese. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dominik Jacob
- Institut für Pharmazie und BiochemieJohannes Gutenberg Universität Mainz Staudingerweg 5 55128 Mainz Deutschland
| | - Kathrin Thüring
- Institut für Pharmazie und BiochemieJohannes Gutenberg Universität Mainz Staudingerweg 5 55128 Mainz Deutschland
| | - Aurellia Galliot
- Institut für Pharmazie und BiochemieJohannes Gutenberg Universität Mainz Staudingerweg 5 55128 Mainz Deutschland
| | - Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Akif Ciftci
- Institut für Biochemie und MolekularbiologieMedizinische FakultätUniversität Freiburg Stefan-Meier-Straße 17 79104 Freiburg Deutschland
| | - Karin Scharmann
- Max Planck Research Group for RNA BiologyMax-Planck-Institute für molekulare Biomedizin Von-Esmarch-Straße 54 48149 Münster Deutschland
| | - Michael Stock
- Institute of Molecular Biology Ackermannweg 4 55128 Mainz Deutschland
| | | | - Sebastian A. Leidel
- Max Planck Research Group for RNA BiologyMax-Planck-Institute für molekulare Biomedizin Von-Esmarch-Straße 54 48149 Münster Deutschland
| | - Yuri Motorin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy Frankreich
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet MikrobiologieUniversität Kassel Heinrich-Plett-Straße 40 34132 Kassel Deutschland
| | - Roland Klassen
- Institut für Biologie, Fachgebiet MikrobiologieUniversität Kassel Heinrich-Plett-Straße 40 34132 Kassel Deutschland
| | - Mark Helm
- Institut für Pharmazie und BiochemieJohannes Gutenberg Universität Mainz Staudingerweg 5 55128 Mainz Deutschland
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12
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Dixit S, Henderson JC, Alfonzo JD. Multi-Substrate Specificity and the Evolutionary Basis for Interdependence in tRNA Editing and Methylation Enzymes. Front Genet 2019; 10:104. [PMID: 30838029 PMCID: PMC6382703 DOI: 10.3389/fgene.2019.00104] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 12/12/2022] Open
Abstract
Among tRNA modification enzymes there is a correlation between specificity for multiple tRNA substrates and heteromultimerization. In general, enzymes that modify a conserved residue in different tRNA sequences adopt a heterodimeric structure. Presumably, such changes in the oligomeric state of enzymes, to gain multi-substrate recognition, are driven by the need to accommodate and catalyze a particular reaction in different substrates while maintaining high specificity. This review focuses on two classes of enzymes where the case for multimerization as a way to diversify molecular recognition can be made. We will highlight several new themes with tRNA methyltransferases and will also discuss recent findings with tRNA editing deaminases. These topics will be discussed in the context of several mechanisms by which heterodimerization may have been achieved during evolution and how these mechanisms might impact modifications in different systems.
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Affiliation(s)
| | | | - Juan D. Alfonzo
- Department of Microbiology, The Ohio State Biochemistry Program, The Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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13
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Paris Z, Alfonzo JD. How the intracellular partitioning of tRNA and tRNA modification enzymes affects mitochondrial function. IUBMB Life 2018; 70:1207-1213. [PMID: 30358065 DOI: 10.1002/iub.1957] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/21/2018] [Indexed: 11/06/2022]
Abstract
Organisms have evolved different strategies to seclude certain molecules to specific locations of the cell. This is most pronounced in eukaryotes with their extensive intracellular membrane systems. Intracellular compartmentalization is particularly critical in genome containing organelles, which because of their bacterial evolutionary ancestry still maintain protein-synthesis machinery that resembles more their evolutionary origin than the extant eukaryotic cell they once joined as an endosymbiont. Despite this, it is clear that genome-containing organelles such as the mitochondria are not in isolation and many molecules make it across the mitochondrial membranes from the cytoplasm. In this realm the import of tRNAs and the enzymes that modify them prove most consequential. In this review, we discuss two recent examples of how modifications typically found in cytoplasmic tRNAs affect mitochondrial translation in organisms that forcibly import all their tRNAs from the cytoplasm. In our view, the combination of tRNA import and the compartmentalization of modification enzymes must have played a critical role in the evolution of the organelle. © 2018 IUBMB Life, 70(12):1207-1213, 2018.
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Affiliation(s)
- Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Juan D Alfonzo
- Department of Microbiology, Ohio State Biochemistry Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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14
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McKenney KM, Alfonzo JD. From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. Life (Basel) 2016; 6:E13. [PMID: 26985907 PMCID: PMC4810244 DOI: 10.3390/life6010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/27/2016] [Accepted: 03/07/2016] [Indexed: 12/13/2022] Open
Abstract
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In the present document, we will attempt to take a chemical rollercoaster ride from prebiotic times to the present, with nucleoside modifications as key players and tRNA as the centerpiece that drove the evolution of biological systems to where we are today. These ideas will be put forth while touching on several examples of tRNA modification enzymes and their modus operandi in cells. In passing, we submit that the choice of tRNA is not a whimsical one but rather highlights its critical function as an essential invention for the evolution of protein enzymes.
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Affiliation(s)
- Katherine M McKenney
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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15
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A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Sci Rep 2016; 6:21438. [PMID: 26888608 PMCID: PMC4757839 DOI: 10.1038/srep21438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/18/2016] [Indexed: 02/06/2023] Open
Abstract
Most eukaryotic ribosomes contain 26/28S, 5S, and 5.8S large subunit ribosomal RNAs (LSU rRNAs) in addition to the 18S rRNA of the small subunit (SSU rRNA). However, in kinetoplastids, a group of organisms that include medically important members of the genus Trypanosoma and Leishmania, the 26/28S large subunit ribosomal RNA is uniquely composed of 6 rRNA fragments. In addition, recent studies have shown the presence of expansion segments in the large ribosomal subunit (60S) of Trypanosoma brucei. Given these differences in structure, processing and assembly, T. brucei ribosomes may require biogenesis factors not found in other organisms. Here, we show that one of two putative 3-methylcytidine methyltransferases, TbMTase37 (a homolog of human methyltransferase-like 6, METTL6), is important for ribosome stability in T. brucei. TbMTase37 localizes to the nucleolus and depletion of the protein results in accumulation of ribosomal particles lacking srRNA 4 and reduced levels of polysome associated ribosomes. We also find that TbMTase37 plays a role in cytokinesis, as loss of the protein leads to multi-flagellated and multi-nucleated cells.
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16
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Abstract
tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, methylation reactions are by far the most abundant. The tRNA methyltransferases comprise a diverse enzyme superfamily, including members of multiple structural classes that appear to have arisen independently during evolution. Even among closely related family members, examples of unusual substrate specificity and chemistry have been observed. Here we review recent advances in tRNA methyltransferase mechanism and function with a particular emphasis on discoveries of alternative substrate specificities and chemistry associated with some methyltransferases. Although the molecular function for a specific tRNA methylation may not always be clear, mutations in tRNA methyltransferases have been increasingly associated with human disease. The impact of tRNA methylation on human biology is also discussed.
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Affiliation(s)
- William E Swinehart
- a Center for RNA Biology and Department of Chemistry and Biochemistry ; Ohio State University ; Columbus , OH USA
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17
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Powell C, Kopajtich R, D’Souza AR, Rorbach J, Kremer L, Husain R, Dallabona C, Donnini C, Alston C, Griffin H, Pyle A, Chinnery P, Strom T, Meitinger T, Rodenburg R, Schottmann G, Schuelke M, Romain N, Haller R, Ferrero I, Haack T, Taylor R, Prokisch H, Minczuk M. TRMT5 Mutations Cause a Defect in Post-transcriptional Modification of Mitochondrial tRNA Associated with Multiple Respiratory-Chain Deficiencies. Am J Hum Genet 2015; 97:319-28. [PMID: 26189817 PMCID: PMC4573257 DOI: 10.1016/j.ajhg.2015.06.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/16/2015] [Indexed: 10/29/2022] Open
Abstract
Deficiencies in respiratory-chain complexes lead to a variety of clinical phenotypes resulting from inadequate energy production by the mitochondrial oxidative phosphorylation system. Defective expression of mtDNA-encoded genes, caused by mutations in either the mitochondrial or nuclear genome, represents a rapidly growing group of human disorders. By whole-exome sequencing, we identified two unrelated individuals carrying compound heterozygous variants in TRMT5 (tRNA methyltransferase 5). TRMT5 encodes a mitochondrial protein with strong homology to members of the class I-like methyltransferase superfamily. Both affected individuals presented with lactic acidosis and evidence of multiple mitochondrial respiratory-chain-complex deficiencies in skeletal muscle, although the clinical presentation of the two affected subjects was remarkably different; one presented in childhood with failure to thrive and hypertrophic cardiomyopathy, and the other was an adult with a life-long history of exercise intolerance. Mutations in TRMT5 were associated with the hypomodification of a guanosine residue at position 37 (G37) of mitochondrial tRNA; this hypomodification was particularly prominent in skeletal muscle. Deficiency of the G37 modification was also detected in human cells subjected to TRMT5 RNAi. The pathogenicity of the detected variants was further confirmed in a heterologous yeast model and by the rescue of the molecular phenotype after re-expression of wild-type TRMT5 cDNA in cells derived from the affected individuals. Our study highlights the importance of post-transcriptional modification of mitochondrial tRNAs for faithful mitochondrial function.
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18
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Torres AG, Piñeyro D, Rodríguez-Escribà M, Camacho N, Reina O, Saint-Léger A, Filonava L, Batlle E, Ribas de Pouplana L. Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. Nucleic Acids Res 2015; 43:5145-57. [PMID: 25916855 PMCID: PMC4446420 DOI: 10.1093/nar/gkv277] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022] Open
Abstract
Transfer RNAs (tRNAs) are key adaptor molecules of the genetic code that are heavily modified post-transcriptionally. Inosine at the first residue of the anticodon (position 34; I34) is an essential widespread tRNA modification that has been poorly studied thus far. The modification in eukaryotes results from a deamination reaction of adenine that is catalyzed by the heterodimeric enzyme adenosine deaminase acting on tRNA (hetADAT), composed of two subunits: ADAT2 and ADAT3. Using high-throughput small RNA sequencing (RNAseq), we show that this modification is incorporated to human tRNAs at the precursor tRNA level and during maturation. We also functionally validated the human genes encoding for hetADAT and show that the subunits of this enzyme co-localize in nucleus in an ADAT2-dependent manner. Finally, by knocking down HsADAT2, we demonstrate that variations in the cellular levels of hetADAT will result in changes in the levels of I34 modification in all its potential substrates. Altogether, we present RNAseq as a powerful tool to study post-transcriptional tRNA modifications at the precursor tRNA level and give the first insights on the biology of I34 tRNA modification in metazoans.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - David Piñeyro
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Adélaïde Saint-Léger
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, Barcelona, 08010 Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, Barcelona, 08010 Catalonia, Spain
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19
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Sample PJ, Kořený L, Paris Z, Gaston KW, Rubio MAT, Fleming IMC, Hinger S, Horáková E, Limbach PA, Lukeš J, Alfonzo JD. A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria. Nucleic Acids Res 2015; 43:4262-73. [PMID: 25845597 PMCID: PMC4417183 DOI: 10.1093/nar/gkv286] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 03/24/2015] [Indexed: 01/14/2023] Open
Abstract
Establishment of the early genetic code likely required strategies to ensure translational accuracy and inevitably involved tRNA post-transcriptional modifications. One such modification, wybutosine/wyosine is crucial for translational fidelity in Archaea and Eukarya; yet it does not occur in Bacteria and has never been described in mitochondria. Here, we present genetic, molecular and mass spectromery data demonstrating the first example of wyosine in mitochondria, a situation thus far unique to kinetoplastids. We also show that these modifications are important for mitochondrial function, underscoring their biological significance. This work focuses on TyW1, the enzyme required for the most critical step of wyosine biosynthesis. Based on molecular phylogeny, we suggest that the kinetoplastids pathways evolved via gene duplication and acquisition of an FMN-binding domain now prevalent in TyW1 of most eukaryotes. These findings are discussed in the context of the extensive U-insertion RNA editing in trypanosome mitochondria, which may have provided selective pressure for maintenance of mitochondrial wyosine in this lineage.
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Affiliation(s)
- Paul J Sample
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Luděk Kořený
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kirk W Gaston
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Mary Anne T Rubio
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ian M C Fleming
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Scott Hinger
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Eva Horáková
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic Canadian Institute For Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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20
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Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z, Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. Malleable mitochondrion of Trypanosoma brucei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:73-151. [PMID: 25708462 DOI: 10.1016/bs.ircmb.2014.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The importance of mitochondria for a typical aerobic eukaryotic cell is undeniable, as the list of necessary mitochondrial processes is steadily growing. Here, we summarize the current knowledge of mitochondrial biology of an early-branching parasitic protist, Trypanosoma brucei, a causative agent of serious human and cattle diseases. We present a comprehensive survey of its mitochondrial pathways including kinetoplast DNA replication and maintenance, gene expression, protein and metabolite import, major metabolic pathways, Fe-S cluster synthesis, ion homeostasis, organellar dynamics, and other processes. As we describe in this chapter, the single mitochondrion of T. brucei is everything but simple and as such rivals mitochondria of multicellular organisms.
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Affiliation(s)
- Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Present address: Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Germany
| | - Corinna Benz
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Sameer Dixit
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Zhenqiu Huang
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Lucie Ridlon
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Salk Institute, La Jolla, San Diego, USA
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - David Wildridge
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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21
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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22
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Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H. The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process. J Biol Chem 2013; 288:25562-25574. [PMID: 23867454 DOI: 10.1074/jbc.m113.485128] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A conserved guanosine at position 18 (G18) in the D-loop of tRNAs is often modified to 2'-O-methylguanosine (Gm). Formation of Gm18 in eubacterial tRNA is catalyzed by tRNA (Gm18) methyltransferase (TrmH). TrmH enzymes can be divided into two types based on their substrate tRNA specificity. Type I TrmH, including Thermus thermophilus TrmH, can modify all tRNA species, whereas type II TrmH, for example Escherichia coli TrmH, modifies only a subset of tRNA species. Our previous crystal study showed that T. thermophilus TrmH is a class IV S-adenosyl-l-methionine-dependent methyltransferase, which maintains a topological knot structure in the catalytic domain. Because TrmH enzymes have short stretches at the N and C termini instead of a clear RNA binding domain, these stretches are believed to be involved in tRNA recognition. In this study, we demonstrate by site-directed mutagenesis that both N- and C-terminal regions function in tRNA binding. However, in vitro and in vivo chimera protein studies, in which four chimeric proteins of type I and II TrmHs were used, demonstrated that the catalytic domain discriminates substrate tRNAs from nonsubstrate tRNAs. Thus, the N- and C-terminal regions do not function in the substrate tRNA discrimination process. Pre-steady state analysis of complex formation between mutant TrmH proteins and tRNA by stopped-flow fluorescence measurement revealed that the C-terminal region works in the initial binding process, in which nonsubstrate tRNA is not excluded, and that structural movement of the motif 2 region of the catalytic domain in an induced-fit process is involved in substrate tRNA discrimination.
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Affiliation(s)
- Anna Ochi
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Koki Makabe
- the Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Ryota Yamagami
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Akira Hirata
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Reiko Sakaguchi
- the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Ya-Ming Hou
- the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Kazunori Watanabe
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Osamu Nureki
- the Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan, and
| | - Kunihiro Kuwajima
- the Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Hiroyuki Hori
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan,; the Venture Business Laboratory, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan.
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