101
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Dou L, Zhou W, Zhang L, Xu L, Han K. Accurate identification of RNA D modification using multiple features. RNA Biol 2021; 18:2236-2246. [PMID: 33729104 PMCID: PMC8632091 DOI: 10.1080/15476286.2021.1898160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 10/21/2022] Open
Abstract
As one of the common post-transcriptional modifications in tRNAs, dihydrouridine (D) has prominent effects on regulating the flexibility of tRNA as well as cancerous diseases. Facing with the expensive and time-consuming sequencing techniques to detect D modification, precise computational tools can largely promote the progress of molecular mechanisms and medical developments. We proposed a novel predictor, called iRNAD_XGBoost, to identify potential D sites using multiple RNA sequence representations. In this method, by considering the imbalance problem using hybrid sampling method SMOTEEEN, the XGBoost-selected top 30 features are applied to construct model. The optimized model showed high Sn and Sp values of 97.13% and 97.38% over jackknife test, respectively. For the independent experiment, these two metrics separately achieved 91.67% and 94.74%. Compared with iRNAD method, this model illustrated high generalizability and consistent prediction efficiencies for positive and negative samples, which yielded satisfactory MCC scores of 0.94 and 0.86, respectively. It is inferred that the chemical property and nucleotide density features (CPND), electron-ion interaction pseudopotential (EIIP and PseEIIP) as well as dinucleotide composition (DNC) are crucial to the recognition of D modification. The proposed predictor is a promising tool to help experimental biologists investigate molecular functions.
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Affiliation(s)
- Lijun Dou
- School of Automotive and Transportation Engineering, Shenzhen Polytechnic, Shenzhen, GuangdongChina
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, SichuanChina
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, HeilongjiangChina
| | - Lichao Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, Guangdong, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, GuangdongChina
| | - Ke Han
- School of Computer and Information Engineering, Harbin University of Commerce, Harbin, HeilongjiangChina
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102
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Wang N, Dong WL, Zhang XJ, Zhou T, Huang XJ, Li BG, Liu JN, Ma XF, Li ZH. Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs. PLANTA 2021; 254:116. [PMID: 34750674 DOI: 10.1007/s00425-021-03775-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The novel structural variations were identified in cotton chloroplast tRNAs and gene loss events were more obvious than duplications in chloroplast tRNAs. Transfer RNAs (tRNA) have long been believed an evolutionary-conserved molecular family, which play the key roles in the process of protein biosynthesis in plant life activities. In this study, we detected the evolutionary characteristics and phylogeny of chloroplast tRNAs in cotton plants, an economic and fibered important taxon in the world. We firstly annotated the chloroplast tRNAs of 27 Gossypium species to analyze their genetic composition, structural characteristics and evolution. Compared with the traditional view of evolutionary conservation of tRNA, some novel tRNA structural variations were identified in cotton plants. I.g., tRNAVal-UAC and tRNAIle-GAU only contained one intron in the anti-condon loop region of tRNA secondary structure, respectively. In the variable region, some tRNAs contained a circle structure with a few nucleotides. Interestingly, the calculation result of free energy indicated that the variation of novel tRNAs contributed to the stability of tRNA structure. Phylogenetic analysis suggested that chloroplast tRNAs have evolved from multiple common ancestors, and the tRNAMet seemed to be an ancestral tRNA, which can be duplicated and diversified to produce other tRNAs. The chloroplast tRNAs contained a group I intron in cotton plants, and the evolutionary analysis of introns indicated that group I intron of chloroplast tRNA originated from cyanobacteria. Analysis of gene duplication and loss events showed that gene loss events were more obvious than duplications in Gossypium chloroplast tRNAs. Additionally, we found that the rate of transition was higher than the ones of transversion in cotton chloroplast tRNAs. This study provided new insights into the structural characteristics and evolution of chloroplast tRNAs in cotton plants.
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Affiliation(s)
- Ning Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Wan-Lin Dong
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiao-Jing Zhang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tong Zhou
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiao-Juan Huang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jian-Ni Liu
- State Key Laboratory of Continental Dynamics, Department of Geology, Early Life Institute, Northwest University, Xi'an, 710069, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhong-Hu Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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103
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Liu C, Yuan J, Zhang X, Jin S, Li F, Xiang J. tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis. Open Biol 2021; 11:210190. [PMID: 34753322 PMCID: PMC8580430 DOI: 10.1098/rsob.210190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Using the sea cucumber Apostichopus japonicus as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic non-coding RNAs, transfer RNAs (tRNAs) tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence, which might be a compromise between functionality and translation efficiency for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of A. japonicus was positively correlated with amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitates their saponin synthesis and survival using food resources with low nutrient content.
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Affiliation(s)
- Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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104
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Abuduaini A, Wang YB, Zhou HY, Kang RP, Ding ML, Jiang Y, Suo FY, Huang LD. The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species. IMA Fungus 2021; 12:31. [PMID: 34670626 PMCID: PMC8527695 DOI: 10.1186/s43008-021-00081-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: 09/04/2020] [Accepted: 10/10/2021] [Indexed: 01/06/2023] Open
Abstract
In this study, the complete mitochondrial genome of O. gracilis was sequenced and assembled before being compared with related species. As the second largest mitogenome reported in the family Ophiocordycipitaceae, the mitogenome of O. gracilis (voucher OG201301) is a circular DNA molecule of 134,288 bp that contains numerous introns and longer intergenomic regions. UCA was detected as anticodon in tRNA-Sec of O. gracilis, while comparative mitogenome analysis of nine Ophiocordycipitaceae fungi indicated that the order and contents of PCGs and rRNA genes were considerably conserved and could descend from a common ancestor in Ophiocordycipitaceae. In addition, the expansion of mitochondrial organization, introns, gene length, and order of O. gracilis were determined to be similar to those of O. sinensis, which indicated common mechanisms underlying adaptive evolution in O. gracilis and O. sinensis. Based on the mitochondrial gene dataset (15 PCGs and 2 RNA genes), a close genetic relationship between O. gracilis and O. sinensis was revealed through phylogenetic analysis. This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. Based on the obtained results, the mitogenome of O. gracilis can increase understanding of the genetic diversity and evolution of cordycipitoid fungi.
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Affiliation(s)
- Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Yuan-Bing Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hui-Ying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Rui-Ping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Ming-Liang Ding
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Fei-Ya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Luo-Dong Huang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China. .,Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, Nanning, 530004, China.
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105
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Dynamic changes in tRNA modifications and abundance during T cell activation. Proc Natl Acad Sci U S A 2021; 118:2106556118. [PMID: 34642250 DOI: 10.1073/pnas.2106556118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA (transfer RNA) supply and mRNA (messenger RNA) demand during cancerous proliferation. Yet dynamic changes may also occur during physiologically normal proliferation, and these are less well characterized. We examined the tRNA and mRNA pools of T cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observed a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool relaxed back to the basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T cell activation. These modifications occur in the anticodon loops of two tRNAs that decode "slippery codons," which are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with an HIV gag-pol frameshifting site reporter. These results may explain HIV's specific tropism toward proliferating T cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a layer of translation regulation during T cell proliferation and expose a potential tradeoff between cellular growth and translation fidelity.
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106
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Das AS, Alfonzo JD, Accornero F. The importance of RNA modifications: From cells to muscle physiology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1700. [PMID: 34664402 DOI: 10.1002/wrna.1700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022]
Abstract
Naturally occurring post-transcriptional chemical modifications serve critical roles in impacting RNA structure and function. More directly, modifications may affect RNA stability, intracellular transport, translational efficiency, and fidelity. The combination of effects caused by modifications are ultimately linked to gene expression regulation at a genome-wide scale. The latter is especially true in systems that undergo rapid metabolic and or translational remodeling in response to external stimuli, such as the presence of stressors, but beyond that, modifications may also affect cell homeostasis. Although examples of the importance of RNA modifications in translation are accumulating rapidly, still what these contribute to the function of complex physiological systems such as muscle is only recently emerging. In the present review, we will introduce key information on various modifications and highlight connections between those and cellular malfunctions. In passing, we will describe well-documented roles for modifications in the nervous system and use this information as a stepping stone to emphasize a glaring paucity of knowledge on the role of RNA modifications in heart and skeletal muscle, with particular emphasis on mitochondrial function in those systems. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Anindhya Sundar Das
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA.,The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Federica Accornero
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA.,The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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107
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Bian M, Huang S, Yu D, Zhou Z. tRNA Metabolism and Lung Cancer: Beyond Translation. Front Mol Biosci 2021; 8:659388. [PMID: 34660690 PMCID: PMC8516113 DOI: 10.3389/fmolb.2021.659388] [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: 01/27/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer, one of the most malignant tumors, has extremely high morbidity and mortality, posing a serious threat to global health. It is an urgent need to fully understand the pathogenesis of lung cancer and provide new ideas for its treatment. Interestingly, accumulating evidence has identified that transfer RNAs (tRNAs) and tRNA metabolism–associated enzymes not only participate in the protein translation but also play an important role in the occurrence and development of lung cancer. In this review, we summarize the different aspects of tRNA metabolism in lung cancer, such as tRNA transcription and mutation, tRNA molecules and derivatives, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (ARSs), aiming at a better understanding of the pathogenesis of lung cancer and providing new therapeutic strategies for it.
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Affiliation(s)
- Meng Bian
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shiqiong Huang
- Department of Pharmacy, The First Hospital of Changsha, Changsha, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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108
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Zhao YH, Zhou T, Wang JX, Li Y, Fang MF, Liu JN, Li ZH. Evolution and structural variations in chloroplast tRNAs in gymnosperms. BMC Genomics 2021; 22:750. [PMID: 34663228 PMCID: PMC8524817 DOI: 10.1186/s12864-021-08058-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/06/2021] [Indexed: 11/22/2022] Open
Abstract
Background Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. Results In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3′ CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. Conclusions These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08058-3.
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Affiliation(s)
- Yu-He Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tong Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jiu-Xia Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yan Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jian-Ni Liu
- State Key Laboratory of Continental Dynamics, Department of Geology, Early Life Institute, Northwest University, Xi'an, 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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109
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Sekulovski S, Devant P, Panizza S, Gogakos T, Pitiriciu A, Heitmeier K, Ramsay EP, Barth M, Schmidt C, Tuschl T, Baas F, Weitzer S, Martinez J, Trowitzsch S. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Nat Commun 2021; 12:5610. [PMID: 34584079 PMCID: PMC8479045 DOI: 10.1038/s41467-021-25870-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Introns of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15–34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes. Mutations within subunits of the tRNA splicing endonuclease complex (TSEN) are associated with pontocerebellar hypoplasia (PCH). Here the authors show that tRNA intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers, and provide evidence that modulation of TSEN stability may contribute to PCH phenotypes.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Pascal Devant
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.,Ph.D. Program in Virology, Harvard Medical School, Boston, MA, USA.,Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Silvia Panizza
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Tasos Gogakos
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Anda Pitiriciu
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Katharina Heitmeier
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | | | - Marie Barth
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Frank Baas
- Department of Clinical Genetics, Leiden University, Leiden, Netherlands
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.
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110
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Emerging Functions for snoRNAs and snoRNA-Derived Fragments. Int J Mol Sci 2021; 22:ijms221910193. [PMID: 34638533 PMCID: PMC8508363 DOI: 10.3390/ijms221910193] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
The widespread implementation of mass sequencing has revealed a diverse landscape of small RNAs derived from larger precursors. Whilst many of these are likely to be byproducts of degradation, there are nevertheless metabolically stable fragments derived from tRNAs, rRNAs, snoRNAs, and other non-coding RNA, with a number of examples of the production of such fragments being conserved across species. Coupled with specific interactions to RNA-binding proteins and a growing number of experimentally reported examples suggesting function, a case is emerging whereby the biological significance of small non-coding RNAs extends far beyond miRNAs and piRNAs. Related to this, a similarly complex picture is emerging of non-canonical roles for the non-coding precursors, such as for snoRNAs that are also implicated in such areas as the silencing of gene expression and the regulation of alternative splicing. This is in addition to a body of literature describing snoRNAs as an additional source of miRNA-like regulators. This review seeks to highlight emerging roles for such non-coding RNA, focusing specifically on “new” roles for snoRNAs and the small fragments derived from them.
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111
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Bacterial translation machinery for deliberate mistranslation of the genetic code. Proc Natl Acad Sci U S A 2021; 118:2110797118. [PMID: 34413202 DOI: 10.1073/pnas.2110797118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inaccurate expression of the genetic code, also known as mistranslation, is an emerging paradigm in microbial studies. Growing evidence suggests that many microbial pathogens can deliberately mistranslate their genetic code to help invade a host or evade host immune responses. However, discovering different capacities for deliberate mistranslation remains a challenge because each group of pathogens typically employs a unique mistranslation mechanism. In this study, we address this problem by studying duplicated genes of aminoacyl-transfer RNA (tRNA) synthetases. Using bacterial prolyl-tRNA synthetase (ProRS) genes as an example, we identify an anomalous ProRS isoform, ProRSx, and a corresponding tRNA, tRNAProA, that are predominately found in plant pathogens from Streptomyces species. We then show that tRNAProA has an unusual hybrid structure that allows this tRNA to mistranslate alanine codons as proline. Finally, we provide biochemical, genetic, and mass spectrometric evidence that cells which express ProRSx and tRNAProA can translate GCU alanine codons as both alanine and proline. This dual use of alanine codons creates a hidden proteome diversity due to stochastic Ala→Pro mutations in protein sequences. Thus, we show that important plant pathogens are equipped with a tool to alter the identity of their sense codons. This finding reveals the initial example of a natural tRNA synthetase/tRNA pair for dedicated mistranslation of sense codons.
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112
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Fang Y, Liu Y, Yan Y, Shen Y, Li Z, Li X, Zhang Y, Xue Z, Peng C, Chen X, Cao K, Zhou J. Differential Expression Profiles and Function Predictions for tRFs & tiRNAs in Skin Injury Induced by Ultraviolet Irradiation. Front Cell Dev Biol 2021; 9:707572. [PMID: 34447751 PMCID: PMC8383935 DOI: 10.3389/fcell.2021.707572] [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: 05/10/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
Ultraviolet (UV) radiation is a major environmental factor contributing skin damage. As UV exposure is inevitable, it is necessary to pay attention to the underlying molecular mechanisms of UV-induced skin damage to develop effective therapies. tRNA-derived stress-induced RNAs (tiRNAs) and tRNA-derived fragments (tRFs) are tRNA-derived small RNAs (tsRNAs) that are a novel class of short, non-coding RNAs. However, the functions behind tRFs & tiRNAs in UV-induced skin injury are not yet clear. Firstly, the animal model of ultraviolet irradiation induced skin damage was established. Then the skin samples were preserved for the follow-up experiment. Sequencing was used to screen expression profiles and predict target genes. Compared with normal skin, a total of 31 differentially expressed tRFs & tiRNAs were screened. Among these, 10 tRFs & tiRNAs were shown to be significantly different in expression levels, where there were 4 up-regulated and 6 down-regulated target genes. Bioinformatics analyses revealed potential up-regulated tsRNAs (tRF-Val-AAC-012, tRF-Pro-AGG-012, tRF-Val-CAC-018, tRF-Val-AAC-031) and down-regulated tsRNAs (tRF-Arg-CCT-002, tRF-Trp-TCA-001, tiRNA-Ser-GCT-001, tRF-Gly-CCC-019, tRF-Ala-TGC-001, tRF-Ala-TGC-002). In summary, it was speculated that tRF-Gly-CCC-019 plays an important role in acute skin injury induced by UVB radiation by regulating the ras-related C3 botulinum toxin substrate 1 (Rac1) gene in the WNT signaling pathway. This study provides new insights into the mechanisms and therapeutic targets of UV-induced skin injury.
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Affiliation(s)
- Yuan Fang
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yang Liu
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yu Yan
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yiyu Shen
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zenan Li
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xu Li
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yufang Zhang
- Anyang Tumor Hospital, The Fourth Affiliated Hospital of Henan University of Science and Technology, Anyang, China
| | - Zhigang Xue
- Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Cong Peng
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, China
| | - Xiang Chen
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, China
| | - Ke Cao
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianda Zhou
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
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113
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Katsara O, Schneider RJ. m 7G tRNA modification reveals new secrets in the translational regulation of cancer development. Mol Cell 2021; 81:3243-3245. [PMID: 34416137 PMCID: PMC10883294 DOI: 10.1016/j.molcel.2021.07.030] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Orellana et al. (2021) and Dai et al. (2021) demonstrate that increased m7G modification of a subset of tRNAs by the METTL1/WDR4 complex stabilizes these mRNAs against decay, increases translation efficiency, reduces ribosome pausing, is associated with poor survival in human cancers, and is directly transforming.
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Affiliation(s)
- Olga Katsara
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J Schneider
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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114
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Orellana EA, Liu Q, Yankova E, Pirouz M, De Braekeleer E, Zhang W, Lim J, Aspris D, Sendinc E, Garyfallos DA, Gu M, Ali R, Gutierrez A, Mikutis S, Bernardes GJL, Fischer ES, Bradley A, Vassiliou GS, Slack FJ, Tzelepis K, Gregory RI. METTL1-mediated m 7G modification of Arg-TCT tRNA drives oncogenic transformation. Mol Cell 2021; 81:3323-3338.e14. [PMID: 34352207 PMCID: PMC8380730 DOI: 10.1016/j.molcel.2021.06.031] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 02/02/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023]
Abstract
The emerging "epitranscriptomics" field is providing insights into the biological and pathological roles of different RNA modifications. The RNA methyltransferase METTL1 catalyzes N7-methylguanosine (m7G) modification of tRNAs. Here we find METTL1 is frequently amplified and overexpressed in cancers and is associated with poor patient survival. METTL1 depletion causes decreased abundance of m7G-modified tRNAs and altered cell cycle and inhibits oncogenicity. Conversely, METTL1 overexpression induces oncogenic cell transformation and cancer. Mechanistically, we find increased abundance of m7G-modified tRNAs, in particular Arg-TCT-4-1, and increased translation of mRNAs, including cell cycle regulators that are enriched in the corresponding AGA codon. Accordingly, Arg-TCT expression is elevated in many tumor types and is associated with patient survival, and strikingly, overexpression of this individual tRNA induces oncogenic transformation. Thus, METTL1-mediated tRNA modification drives oncogenic transformation through a remodeling of the mRNA "translatome" to increase expression of growth-promoting proteins and represents a promising anti-cancer target.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eliza Yankova
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Storm Therapeutics Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Wencai Zhang
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jihoon Lim
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - Erdem Sendinc
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dimitrios A Garyfallos
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Muxin Gu
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Raja Ali
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sigitas Mikutis
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Allan Bradley
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Frank J Slack
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Konstantinos Tzelepis
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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115
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Gutman T, Goren G, Efroni O, Tuller T. Estimating the predictive power of silent mutations on cancer classification and prognosis. NPJ Genom Med 2021; 6:67. [PMID: 34385450 PMCID: PMC8361094 DOI: 10.1038/s41525-021-00229-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
In recent years it has been shown that silent mutations, in and out of the coding region, can affect gene expression and may be related to tumorigenesis and cancer cell fitness. However, the predictive ability of these mutations for cancer type diagnosis and prognosis has not been evaluated yet. In the current study, based on the analysis of 9,915 cancer genomes and approximately three million mutations, we provide a comprehensive quantitative evaluation of the predictive power of various types of silent and non-silent mutations over cancer classification and prognosis. The results indicate that silent-mutation models outperform the equivalent null models in classifying all examined cancer types and in estimating the probability of survival 10 years after the initial diagnosis. Additionally, combining both non-silent and silent mutations achieved the best classification results for 68% of the cancer types and the best survival estimation results for up to nine years after the diagnosis. Thus, silent mutations hold considerable predictive power over both cancer classification and prognosis, most likely due to their effect on gene expression. It is highly advised that silent mutations are integrated in cancer research in order to unravel the full genomic landscape of cancer and its ramifications on cancer fitness.
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Affiliation(s)
- Tal Gutman
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Guy Goren
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Omri Efroni
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel.
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116
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Ma X, Liu C, Cao X. Plant transfer RNA-derived fragments: Biogenesis and functions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1399-1409. [PMID: 34114725 DOI: 10.1111/jipb.13143] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/10/2021] [Indexed: 06/12/2023]
Abstract
Processing of mature transfer RNAs (tRNAs) produces complex populations of tRNA-derived fragments (tRFs). Emerging evidence shows that tRFs have important functions in bacteria, animals, and plants. Here, we review recent advances in understanding plant tRFs, focusing on their biological and cellular functions, such as regulating stress responses, mediating plant-pathogen interactions, and modulating post-transcriptional gene silencing and translation. We also review sequencing strategies and bioinformatics resources for studying tRFs in plants. Finally, we discuss future directions for plant tRF research, which will expand our knowledge of plant non-coding RNAs.
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Affiliation(s)
- Xuan Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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117
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He Q, He X, Xiao Y, Zhao Q, Ye Z, Cui L, Chen Y, Guan MX. Tissue-specific expression atlas of murine mitochondrial tRNAs. J Biol Chem 2021; 297:100960. [PMID: 34265302 PMCID: PMC8342785 DOI: 10.1016/j.jbc.2021.100960] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/04/2021] [Accepted: 07/12/2021] [Indexed: 11/08/2022] Open
Abstract
Mammalian mitochondrial tRNA (mt-tRNA) plays a central role in the synthesis of the 13 subunits of the oxidative phosphorylation complex system (OXPHOS). However, many aspects of the context-dependent expression of mt-tRNAs in mammals remain unknown. To investigate the tissue-specific effects of mt-tRNAs, we performed a comprehensive analysis of mitochondrial tRNA expression across five mice tissues (brain, heart, liver, skeletal muscle, and kidney) using Northern blot analysis. Striking differences in the tissue-specific expression of 22 mt-tRNAs were observed, in some cases differing by as much as tenfold from lowest to highest expression levels among these five tissues. Overall, the heart exhibited the highest levels of mt-tRNAs, while the liver displayed markedly lower levels. Variations in the levels of mt-tRNAs showed significant correlations with total mitochondrial DNA (mtDNA) contents in these tissues. However, there were no significant differences observed in the 2-thiouridylation levels of tRNALys, tRNAGlu, and tRNAGln among these tissues. A wide range of aminoacylation levels for 15 mt-tRNAs occurred among these five tissues, with skeletal muscle and kidneys most notably displaying the highest and lowest tRNA aminoacylation levels, respectively. Among these tissues, there was a negative correlation between variations in mt-tRNA aminoacylation levels and corresponding variations in mitochondrial tRNA synthetases (mt-aaRS) expression levels. Furthermore, the variable levels of OXPHOS subunits, as encoded by mtDNA or nuclear genes, may reflect differences in relative functional emphasis for mitochondria in each tissue. Our findings provide new insight into the mechanism of mt-tRNA tissue-specific effects on oxidative phosphorylation.
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Affiliation(s)
- Qiufen He
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiao He
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun Xiao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiong Zhao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhenzhen Ye
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Limei Cui
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ye Chen
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Zhejiang Univrsity, Hangzhou, Zhejiang, China.
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Zhejiang Univrsity, Hangzhou, Zhejiang, China; Key Lab of Reproductive Genetics, Center for Mitochondrial Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang, China; Division of Mitochondrial Biomedicine, Zhejiang University-University of Toronto Joint Institute of Genetics and Genome Medicine, Hangzhou, Zhejiang, China.
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118
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Wang J, Dong PK, Xu XF, Huang T, Mao S, Wang QG, Hao J, Liu XH, Sun XD, Kang K, Zhang Q, Li JT, Wang T. Identification of tRNA-derived Fragments and Their Potential Roles in Atherosclerosis. Curr Med Sci 2021; 41:712-721. [PMID: 34403096 DOI: 10.1007/s11596-021-2406-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Atherosclerosis (AS), a chronic inflammatory disease, is the basis of cardiovascular disease (CVD). Although the treatment has been greatly improved, AS still imposes a large burden on human health and the medical system, and we still need to further study its pathogenesis. As a novel biomolecule, transfer RNA-derived fragments (tRFs) play a key role in the progression of various disease. However, whether tRFs contribute to atherosclerosis pathogenesis remains unexplored. METHODS With deep sequencing technology, the change of tRFs expression profiles in patients with AS compared to healthy control group was identified. The accuracy of the sequencing data was validated using RT qPCR. Subsequently, we predicted the potential target genes of tRFs by online miRNA target prediction algorithms. The potential functions of tRFs were evaluated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. RESULTS There were 13 tRFs differentially expressed between patients with AS and healthy controls, of which 2 were up-regulated and 11 were down-regulated. Validation by RT-qPCR analysis confirmed the sequencing results, and tRF-Gly-GCC-009 was highly up-regulated in the AS group based on the results of sequencing which was confirmed by RT-qPCR analysis. Furthermore, GO enrichment and KEGG pathway analyses indicated that 10 signaling pathways were related to tRF-Gly-GCC-009. These pathways might be physiopathological fundamentals of AS, mainly involving in Apelin signaling, Notch signaling and calcium signaling. CONCLUSION The results of our study provide important novel insight into the underlying pathogenesis and demonstrate that tRFs might be potential biomarkers and therapeutic targets for AS in the future.
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Affiliation(s)
- Jian Wang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Pei-Kang Dong
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Xiu-Feng Xu
- Department of Neurology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Tao Huang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Shuai Mao
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Qing-Guo Wang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Jie Hao
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Xiao-Hong Liu
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Xiao-Dong Sun
- Department of Endocrinology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Kai Kang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Quan Zhang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Jing-Tian Li
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China.
| | - Tao Wang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China.
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119
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N 7-Methylguanosine tRNA modification enhances oncogenic mRNA translation and promotes intrahepatic cholangiocarcinoma progression. Mol Cell 2021; 81:3339-3355.e8. [PMID: 34352206 DOI: 10.1016/j.molcel.2021.07.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/08/2021] [Accepted: 07/04/2021] [Indexed: 12/12/2022]
Abstract
Cancer cells selectively promote translation of specific oncogenic transcripts to facilitate cancer survival and progression, but the underlying mechanisms are poorly understood. Here, we find that N7-methylguanosine (m7G) tRNA modification and its methyltransferase complex components, METTL1 and WDR4, are significantly upregulated in intrahepatic cholangiocarcinoma (ICC) and associated with poor prognosis. We further reveal the critical role of METTL1/WDR4 in promoting ICC cell survival and progression using loss- and gain-of-function assays in vitro and in vivo. Mechanistically, m7G tRNA modification selectively regulates the translation of oncogenic transcripts, including cell-cycle and epidermal growth factor receptor (EGFR) pathway genes, in m7G-tRNA-decoded codon-frequency-dependent mechanisms. Moreover, using overexpression and knockout mouse models, we demonstrate the crucial oncogenic function of Mettl1-mediated m7G tRNA modification in promoting ICC tumorigenesis and progression in vivo. Our study uncovers the important physiological function and mechanism of METTL1-mediated m7G tRNA modification in the regulation of oncogenic mRNA translation and cancer progression.
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120
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Ramos-Morales E, Bayam E, Del-Pozo-Rodríguez J, Salinas-Giegé T, Marek M, Tilly P, Wolff P, Troesch E, Ennifar E, Drouard L, Godin JD, Romier C. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic Acids Res 2021; 49:6529-6548. [PMID: 34057470 PMCID: PMC8216470 DOI: 10.1093/nar/gkab436] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/26/2023] Open
Abstract
Post-transcriptional modification of tRNA wobble adenosine into inosine is crucial for decoding multiple mRNA codons by a single tRNA. The eukaryotic wobble adenosine-to-inosine modification is catalysed by the ADAT (ADAT2/ADAT3) complex that modifies up to eight tRNAs, requiring a full tRNA for activity. Yet, ADAT catalytic mechanism and its implication in neurodevelopmental disorders remain poorly understood. Here, we have characterized mouse ADAT and provide the molecular basis for tRNAs deamination by ADAT2 as well as ADAT3 inactivation by loss of catalytic and tRNA-binding determinants. We show that tRNA binding and deamination can vary depending on the cognate tRNA but absolutely rely on the eukaryote-specific ADAT3 N-terminal domain. This domain can rotate with respect to the ADAT catalytic domain to present and position the tRNA anticodon-stem-loop correctly in ADAT2 active site. A founder mutation in the ADAT3 N-terminal domain, which causes intellectual disability, does not affect tRNA binding despite the structural changes it induces but most likely hinders optimal presentation of the tRNA anticodon-stem-loop to ADAT2.
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Affiliation(s)
- Elizabeth Ramos-Morales
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Efil Bayam
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Jordi Del-Pozo-Rodríguez
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Martin Marek
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Peggy Tilly
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Edouard Troesch
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Eric Ennifar
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Juliette D Godin
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Christophe Romier
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
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121
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Fagan SG, Helm M, Prehn JHM. tRNA-derived fragments: A new class of non-coding RNA with key roles in nervous system function and dysfunction. Prog Neurobiol 2021; 205:102118. [PMID: 34245849 DOI: 10.1016/j.pneurobio.2021.102118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
tRNA-derived small RNAs (tsRNA) are a recently identified family of non-coding RNA that have been associated with a variety of cellular functions including the regulation of protein translation and gene expression. Recent sequencing and bioinformatic studies have identified the broad spectrum of tsRNA in the nervous system and demonstrated that this new class of non-coding RNA is produced from tRNA by specific cleavage events catalysed by ribonucleases such as angiogenin and dicer. Evidence is also accumulating that production of tsRNA is increased during disease processes where they regulate stress responses, proteostasis, and neuronal survival. Mutations to tRNA cleaving and modifying enzymes have been implicated in several neurodegenerative disorders, and tsRNA levels in the blood are advancing as biomarkers for neurological disease. In this review we summarize the physiological importance of tsRNA in the central nervous system and their relevance to neurological disease.
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Affiliation(s)
- Steven G Fagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences - IPBS, Johannes Gutenberg-University, 55128, Mainz, Germany
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.
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122
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Beznosková P, Bidou L, Namy O, Valášek LS. Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines. Nucleic Acids Res 2021; 49:5202-5215. [PMID: 34009360 PMCID: PMC8136774 DOI: 10.1093/nar/gkab315] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
Regulation of translation via stop codon readthrough (SC-RT) expands not only tissue-specific but also viral proteomes in humans and, therefore, represents an important subject of study. Understanding this mechanism and all involved players is critical also from a point of view of prospective medical therapies of hereditary diseases caused by a premature termination codon. tRNAs were considered for a long time to be just passive players delivering amino acid residues according to the genetic code to ribosomes without any active regulatory roles. In contrast, our recent yeast work identified several endogenous tRNAs implicated in the regulation of SC-RT. Swiftly emerging studies of human tRNA-ome also advocate that tRNAs have unprecedented regulatory potential. Here, we developed a universal U6 promotor-based system expressing various human endogenous tRNA iso-decoders to study consequences of their increased dosage on SC-RT employing various reporter systems in vivo. This system combined with siRNA-mediated downregulations of selected aminoacyl-tRNA synthetases demonstrated that changing levels of human tryptophan and tyrosine tRNAs do modulate efficiency of SC-RT. Overall, our results suggest that tissue-to-tissue specific levels of selected near-cognate tRNAs may have a vital potential to fine-tune the final landscape of the human proteome, as well as that of its viral pathogens.
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Affiliation(s)
- Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Laure Bidou
- Sorbonne Universités, Paris, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Namy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, the Czech Republic
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123
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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124
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Liu Z, Kim HK, Xu J, Jing Y, Kay MA. The 3'tsRNAs are aminoacylated: Implications for their biogenesis. PLoS Genet 2021; 17:e1009675. [PMID: 34324497 PMCID: PMC8354468 DOI: 10.1371/journal.pgen.1009675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/10/2021] [Accepted: 06/20/2021] [Indexed: 12/03/2022] Open
Abstract
Emerging evidence indicates that tRNA-derived small RNAs (tsRNAs) are involved in fine-tuning gene expression and become dysregulated in various cancers. We recently showed that the 22nt LeuCAG3´tsRNA from the 3´ end of tRNALeu is required for efficient translation of a ribosomal protein mRNA and ribosome biogenesis. Inactivation of this 3´tsRNA induced apoptosis in rapidly dividing cells and suppressed the growth of a patient-derived orthotopic hepatocellular carcinoma in mice. The mechanism involved in the generation of the 3´tsRNAs remains elusive and it is unclear if the 3´-ends of 3´tsRNAs are aminoacylated. Here we report an enzymatic method utilizing exonuclease T to determine the 3´charging status of tRNAs and tsRNAs. Our results showed that the LeuCAG3´tsRNA, and two other 3´tsRNAs are fully aminoacylated. When the leucyl-tRNA synthetase (LARS1) was inhibited, there was no change in the total tRNALeu concentration but a reduction in both the charged tRNALeu and LeuCAG3´tsRNA, suggesting the 3´tsRNAs are fully charged and originated solely from the charged mature tRNA. Altering LARS1 expression or the expression of various tRNALeu mutants were also shown to affect the generation of the LeuCAG3´tsRNA further suggesting they are created in a highly regulated process. The fact that the 3´tsRNAs are aminoacylated and their production is regulated provides additional insights into their importance in post-transcriptional gene regulation that includes coordinating the production of the protein synthetic machinery.
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Affiliation(s)
- Ziwei Liu
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, Califormia, United States of America
| | - Hak Kyun Kim
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, Califormia, United States of America
| | - Jianpeng Xu
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, Califormia, United States of America
| | - Yuqing Jing
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, Califormia, United States of America
| | - Mark A. Kay
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, Califormia, United States of America
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125
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Albers S, Beckert B, Matthies MC, Mandava CS, Schuster R, Seuring C, Riedner M, Sanyal S, Torda AE, Wilson DN, Ignatova Z. Repurposing tRNAs for nonsense suppression. Nat Commun 2021; 12:3850. [PMID: 34158503 PMCID: PMC8219837 DOI: 10.1038/s41467-021-24076-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.
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Affiliation(s)
- Suki Albers
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marco C. Matthies
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Chandra Sekhar Mandava
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Raphael Schuster
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | | | - Maria Riedner
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | - Suparna Sanyal
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew E. Torda
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Daniel N. Wilson
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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126
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Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Syst 2021; 12:771-779.e5. [PMID: 34143976 DOI: 10.1016/j.cels.2021.05.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 01/06/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022]
Abstract
Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p = 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection.
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127
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Shuai J, Shi J, Liang Y, Ji F, Gu L, Yuan Z. Mutational analysis of mitochondrial tRNA genes in 138 patients with Leber's hereditary optic neuropathy. Ir J Med Sci 2021; 191:865-876. [PMID: 34053002 DOI: 10.1007/s11845-021-02656-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Mutations in mitochondrial DNA (mtDNA) are the most important causes for Leber's hereditary optic neuropathy (LHON). Of these, three primary mtDNA mutations account for more than 90% cases of this disease. However, to date, little is known regarding the relationship between mitochondrial tRNA (mt-tRNA) variants and LHON. AIM In this study, we aimed to investigate the association between mt-tRNA variants and LHON. METHODOLOGY One hundred thirty-eight LHON patients lacking three primary mutations (ND1 3460G > A, ND4 11778Gxs > A, and ND6 14484 T > C), as well as 266 controls were enrolled in this study. PCR-Sanger sequencing was performed to screen the mt-tRNA variants. Moreover, the phylogenetic analysis, pathogenicity scoring system, as well as mitochondrial functions were performed. RESULTS We identified 8 possible pathogenic variants: tRNAPhe 593 T > C, tRNALeu(UUR) 3275C > T, tRNAGln 4363 T > C, tRNAMet 4435A > G, tRNAAla 5587 T > C, tRNAGlu 14693A > G, tRNAThr 15927G > A, and 15951A > G, which may change the structural and functional impact on the corresponding tRNAs, and subsequently lead to a failure in tRNA metabolism. Furthermore, significant reductions in mitochondrial ATP and MMP levels and an overproduction of ROS were observed in cybrid cells containing these mt-tRNA variants, suggesting that these variants may lead to mitochondrial dysfunction which was responsible for LHON. CONCLUSION Our study indicated that mt-tRNA variants were associated with LHON, and screening for mt-tRNA variants were recommended for early detection, diagnosis, and prevention of maternally inherited LHON.
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Affiliation(s)
- Jie Shuai
- Department of Ophthalmology, the Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Shi
- Department of Ophthalmology, the Affiliated Hospital of Nantong University, Nantong, China
| | - Ya Liang
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Fangfang Ji
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Luo Gu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Zhilan Yuan
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
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128
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Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes (Basel) 2021; 12:genes12060822. [PMID: 34071968 PMCID: PMC8228828 DOI: 10.3390/genes12060822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
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129
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Li J, Zhu L, Cheng J, Peng Y. Transfer RNA-derived small RNA: A rising star in oncology. Semin Cancer Biol 2021; 75:29-37. [PMID: 34029740 DOI: 10.1016/j.semcancer.2021.05.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023]
Abstract
Transfer RNAs (tRNAs) participate in protein synthesis through delivering amino acids to the ribosome. Nevertheless, recent studies revealed that tRNAs can undergo cleavage by endoribonucleases to generate a heterogeneous class of small RNAs, designated as tRNA-derived small RNAs (tsRNAs). Accumulating evidence demonstrates that tsRNAs play an important role in many biological processes, and their dysregulation is associated with the progression of diseases including cancer. Abnormally expressed tsRNAs contribute to tumor initiation and development through distinct mechanisms, such as transcriptional regulation and RNA interference. In this review, we briefly summarize the current knowledge regarding classification, biogenesis and biological function of tsRNAs. Moreover, we highlight the dysregulation and critical roles of tsRNAs in cancer and discuss their potentials as diagnostic and prognostic biomarkers or therapeutic targets.
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Affiliation(s)
- Jiao Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Lei Zhu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Jian Cheng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China.
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130
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Li C, Jiang Z, Hao J, Liu D, Hu H, Gao Y, Wang D. Role of N6-methyl-adenosine modification in mammalian embryonic development. Genet Mol Biol 2021; 44:e20200253. [PMID: 33999093 PMCID: PMC8127566 DOI: 10.1590/1678-4685-gmb-2020-0253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 04/07/2021] [Indexed: 11/21/2022] Open
Abstract
N6-methyl-adenosine (m6A) methylation is one of the most common and abundant modifications of RNA molecules in eukaryotes. Although various biological roles of m6A methylation have been elucidated, its role in embryonic development is still unclear. In this review, we focused on the function and expression patterns of m6A-related genes in mammalian embryonic development and the role of m6A modification in the embryonic epigenetic reprogramming process. The modification of m6A is regulated by the combined activities of methyltransferases, demethylases, and m6A-binding proteins. m6A-related genes act synergistically to form a dynamic, reversible m6A pattern, which exists in several physiological processes in various stages of embryonic development. The lack of one of these enzymes affects embryonic m6A levels, leading to abnormal embryonic development and even death. Moreover, m6A is a positive regulator of reprogramming to pluripotency and can affect embryo reprogramming by affecting activation of the maternal-to-zygotic transition. In conclusion, m6A is involved in the regulation of gene expression during embryonic development and the metabolic processes of RNA and plays an important role in the epigenetic modification of embryos.
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Affiliation(s)
- Chengshun Li
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Ziping Jiang
- The First Hospital of Jilin University, Department of hand surgery, Changchun, China
| | - Jindong Hao
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Da Liu
- Changchun University of Chinese Medicine, Department of Pharmacy, Changchun, China
| | - Haobo Hu
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Yan Gao
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Dongxu Wang
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
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131
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Abstract
In this issue of Molecular Cell, Behrens et al. (2021) address a long-standing challenge in the field of tRNA regulation and develop an approach for measuring tRNA abundance at unprecedented accuracy.
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Affiliation(s)
- David Wiener
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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132
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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Li HM, Tan X, Zhang S, Yao J, Li HG. Transfer- or 'transmission'-RNA fragments? The roles of tsRNAs in the reproductive system. Mol Hum Reprod 2021; 27:6218776. [PMID: 33837423 DOI: 10.1093/molehr/gaab026] [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] [Received: 01/11/2021] [Revised: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
Transfer-RNAs (tRNAs) help ribosomes decode mRNAs and synthesize proteins; however, tRNA fragments produced under certain conditions, known as tRNA-derived small RNAs (tsRNAs), have been found to play important roles in pathophysiological processes. In the reproductive system, tsRNAs are abundant in gametes and embryos and at the maternal-fetal interface, as well as in microvesicles like epididymosomes, seminal plasma exosomes, and syncytiotrophoblast-derived extracellular vesicles. tsRNAs can affect gamete cell maturation, zygote activation, and early embryonic development. tsRNAs can transmit epigenetic information to later generations. In particular, exposure to environmental factors such as nutrition, isoproterenol, and poly(I:C) may allow tsRNAs to transfer information to the gametes or placenta to alter offspring phenotype. The underlying mechanisms of tsRNAs action include transposon silencing, translation regulation, and target mRNA degradation. Herein, we review the currently reported tsRNAs in the reproductive system, their validated functions, and potential roles. A better understanding of this field may help to provide useful recommendations or develop strategies to increase fertility and conception of healthy babies.
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Affiliation(s)
- Hui-Min Li
- Guilin Medical University, Guilin, P.R. China
| | - Xia Tan
- Center of Reproductive Medicine, Wuhan Union Hospital, Wuhan, P.R. China
| | - Shun Zhang
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Jun Yao
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Hong-Gang Li
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,Genetic Laboratory, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, P.R. China
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134
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McMahon M, Forester C, Buffenstein R. Aging through an epitranscriptomic lens. NATURE AGING 2021; 1:335-346. [PMID: 37117595 DOI: 10.1038/s43587-021-00058-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/08/2021] [Indexed: 04/30/2023]
Abstract
The mechanistic causes of aging, the time-related decline in function and good health that leads to increased mortality, remain poorly understood. Here we propose that age-dependent alteration of the epitranscriptome, encompassing more than 150 chemically distinct post-transcriptional modifications or editing events, warrants exploration as an important modulator of aging. The epitranscriptome is a potent regulator of RNA function, diverse cellular processes and tissue regenerative capacity. To date, only a few studies link alterations in the epitranscriptome to molecular and physiological changes during aging; however, epitranscriptome dysfunction is associated with and underlies several age-associated pathologies, including cancer and neurodegenerative, cardiovascular and autoimmune diseases. For example, changes in RNA modifications (such as N6-methyladenosine and inosine) impact cardiac physiology and are linked to cardiac fibrosis. Although an uncharted research focus, mapping epitranscriptome alterations in the context of aging may elucidate novel predictors of both health and lifespan, and may identify therapeutic targets for attenuating aging and abrogating age-related diseases.
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Affiliation(s)
- Mary McMahon
- Calico Life Sciences LLC, South San Francisco, CA, USA.
| | - Craig Forester
- Department of Pediatrics, University of Colorado, Denver, CO, USA
- Children's Hospital Colorado, Division of Pediatric Hematology/Oncology/Bone Marrow Transplant, Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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135
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Pan X, Geng X, Liu Y, Yu M, Mishra MK, Xu X, Ding X, Liu P, Liang M. Transfer RNA Fragments in the Kidney in Hypertension. Hypertension 2021; 77:1627-1637. [PMID: 33775129 DOI: 10.1161/hypertensionaha.121.16994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiaoqing Pan
- Department of Mathematics, Shanghai Normal University, China (X.P.).,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xuemei Geng
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Manoj K Mishra
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
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136
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Darr J, Tomar A, Lassi M, Gerlini R, Berti L, Hering A, Scheid F, Hrabě de Angelis M, Witting M, Teperino R. iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental Stimuli and Identifies an RNA-Based Endocrine Axis. Cell Rep 2021; 30:3183-3194.e4. [PMID: 32130917 DOI: 10.1016/j.celrep.2020.02.020] [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] [Received: 06/18/2019] [Revised: 12/06/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
Biofluids contain various circulating cell-free RNAs (ccfRNAs). The composition of these ccfRNAs varies among biofluids. They constitute tantalizing biomarker candidates for several pathologies and have been demonstrated to be mediators of cellular communication. Little is known about their function in physiological and developmental settings, and most works are limited to in vitro studies. Here, we develop iTAG-RNA, a method for the unbiased tagging of RNA transcripts in mice in vivo. We use iTAG-RNA to isolate hepatocytes and kidney proximal epithelial cell-specific transcriptional responses to a dietary challenge without interfering with the tissue architecture and to identify multiple hepatocyte-secreted ccfRNAs in plasma. We also identify specific transfer of liver-derived ccfRNAs to adipose tissue and skeletal muscle, where they likely constitute a buffering system to maintain lipid homeostasis under acute high-fat-diet feeding. Our findings directly demonstrate in vivo transfer of RNAs between tissues and highlight its implications for endocrine signaling and homeostasis.
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Affiliation(s)
- Jonatan Darr
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Archana Tomar
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Maximilian Lassi
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Lucia Berti
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Annette Hering
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fabienne Scheid
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Experimental Genetics, Faculty of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Oberschleißheim, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Freising, Germany.
| | - Raffaele Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany.
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137
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Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
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Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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138
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Pereira M, Ribeiro DR, Pinheiro MM, Ferreira M, Kellner S, Soares AR. m 5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Int J Mol Sci 2021; 22:ijms22062941. [PMID: 33799331 PMCID: PMC8001983 DOI: 10.3390/ijms22062941] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
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Affiliation(s)
- Marisa Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Diana R. Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Miguel M. Pinheiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Margarida Ferreira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, 81377 Munich, Germany;
- Institute of Pharmaceutical Chemistry, Goethe-University, 60438 Frankfurt, Germany
| | - Ana R. Soares
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
- Correspondence:
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139
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Nagai A, Mori K, Shiomi Y, Yoshihisa T. OTTER, a new method quantifying absolute amounts of tRNAs. RNA (NEW YORK, N.Y.) 2021; 27:rna.076489.120. [PMID: 33674420 PMCID: PMC8051270 DOI: 10.1261/rna.076489.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/27/2021] [Indexed: 05/03/2023]
Abstract
To maintain optimal proteome, both codon choice of each mRNA and supply of aminoacyl-tRNAs are two principal factors in translation. Recent reports have revealed that the amounts of tRNAs in cells are more dynamic than we had expected. High-throughput methods such as RNA-Seq and microarrays are versatile for comprehensive detection of changes in individual tRNA amounts, but they suffer from inability to assess signal production efficiencies of individual tRNA species. Thus, they are not the perfect choice to measure absolute amounts of tRNAs. Here, we introduce a novel method for this purpose, termed Oligonucleotide-directed Three-prime Terminal Extension of RNA (OTTER), which employs fluorescence-labeling at the 3'-terminus of a tRNA by optimized reverse primer extension and an assessment step of each labeling efficiency by northern blotting. Using this method, we quantified the absolute amounts of the 34 individual and 4 pairs of isoacceptor tRNAs out of the total 42 nuclear-encoded isoacceptors in the yeast Saccharomyces cerevisiae. We found that the amounts of tRNAs in log phase yeast cells grown in a rich glucose medium range from 0.030 to 0.73 pmol/µg RNA. The tRNA amounts seem to be altered at the isoacceptor level by a few folds in response to physiological growing conditions. The data obtained by OTTER are poorly correlated with those by simple RNA-Seq, marginally with those by microarrays and by microscale thermophoresis. However, the OTTER data showed good agreement with the data obtained by 2D-gel analysis of in vivo radiolabeled RNAs. Thus, OTTER is a suitable method for quantifying absolute amounts of tRNAs at the level of isoacceptor resolution.
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Affiliation(s)
- Akihisa Nagai
- Graduate School of Life Science, University of Hyogo
| | - Kohei Mori
- Graduate School of Life Science, University of Hyogo
| | - Yuma Shiomi
- Graduate School of Life Science, University of Hyogo
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140
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Li LJ, Chang WM, Hsiao M. Aberrant Expression of microRNA Clusters in Head and Neck Cancer Development and Progression: Current and Future Translational Impacts. Pharmaceuticals (Basel) 2021; 14:ph14030194. [PMID: 33673471 PMCID: PMC7997248 DOI: 10.3390/ph14030194] [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: 01/07/2021] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs are small non-coding RNAs known to negative regulate endogenous genes. Some microRNAs have high sequence conservation and localize as clusters in the genome. Their coordination is regulated by simple genetic and epigenetic events mechanism. In cells, single microRNAs can regulate multiple genes and microRNA clusters contain multiple microRNAs. MicroRNAs can be differentially expressed and act as oncogenic or tumor suppressor microRNAs, which are based on the roles of microRNA-regulated genes. It is vital to understand their effects, regulation, and various biological functions under both normal and disease conditions. Head and neck squamous cell carcinomas are some of the leading causes of cancer-related deaths worldwide and are regulated by many factors, including the dysregulation of microRNAs and their clusters. In disease stages, microRNA clusters can potentially control every field of oncogenic function, including growth, proliferation, apoptosis, migration, and intercellular commutation. Furthermore, microRNA clusters are regulated by genetic mutations or translocations, transcription factors, and epigenetic modifications. Additionally, microRNA clusters harbor the potential to act therapeutically against cancer in the future. Here, we review recent advances in microRNA cluster research, especially relative to head and neck cancers, and discuss their regulation and biological functions under pathological conditions as well as translational applications.
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Affiliation(s)
- Li-Jie Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - Wei-Min Chang
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-2-2789–8752
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141
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Behrens A, Rodschinka G, Nedialkova DD. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol Cell 2021; 81:1802-1815.e7. [PMID: 33581077 PMCID: PMC8062790 DOI: 10.1016/j.molcel.2021.01.028] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/25/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome these limitations with modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which combines a workflow for full-length cDNA library construction from endogenously modified tRNA with a comprehensive and user-friendly computational analysis toolkit. Our method accurately captures tRNA abundance and modification status in yeast, fly, and human cells and is applicable to any organism with a known genome. We applied mim-tRNAseq to discover a dramatic heterogeneity of tRNA isodecoder pools among diverse human cell lines and a surprising interdependence of modifications at distinct sites within the same tRNA transcript. mim-tRNAseq overcomes experimental and computational hurdles to tRNA quantitation mim-tRNAseq includes a comprehensive computational toolkit for tRNA read analysis tRNA abundance, aminoacylation, and modification status quantified in one reaction mim-tRNAseq reveals an interdependence of modifications at distinct tRNA positions
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Affiliation(s)
- Andrew Behrens
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Geraldine Rodschinka
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Danny D Nedialkova
- Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Chemistry, Technical University of Munich, 85748 Garching, Germany.
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142
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Maran SR, de Lemos Padilha Pitta JL, Dos Santos Vasconcelos CR, McDermott SM, Rezende AM, Silvio Moretti N. Epitranscriptome machinery in Trypanosomatids: New players on the table? Mol Microbiol 2021; 115:942-958. [PMID: 33513291 DOI: 10.1111/mmi.14688] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/20/2022]
Abstract
Trypanosoma and Leishmania parasites cause devastating tropical diseases resulting in serious global health consequences. These organisms have complex life cycles with mammalian hosts and insect vectors. The parasites must, therefore, survive in different environments, demanding rapid physiological and metabolic changes. These responses depend upon regulation of gene expression, which primarily occurs posttranscriptionally. Altering the composition or conformation of RNA through nucleotide modifications is one posttranscriptional mechanism of regulating RNA fate and function, and modifications including N6-methyladenosine (m6A), N1-methyladenosine (m1A), N5-methylcytidine (m5C), N4-acetylcytidine (ac4C), and pseudouridine (Ψ), dynamically regulate RNA stability and translation in diverse organisms. Little is known about RNA modifications and their machinery in Trypanosomatids, but we hypothesize that they regulate parasite gene expression and are vital for survival. Here, we identified Trypanosomatid homologs for writers of m1A, m5C, ac4C, and Ψ and analyze their evolutionary relationships. We systematically review the evidence for their functions and assess their potential use as therapeutic targets. This work provides new insights into the roles of these proteins in Trypanosomatid parasite biology and treatment of the diseases they cause and illustrates that Trypanosomatids provide an excellent model system to study RNA modifications, their molecular, cellular, and biological consequences, and their regulation and interplay.
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Affiliation(s)
- Suellen Rodrigues Maran
- Laboratory of Molecular Biology of Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo, São Paulo, Brazil
| | | | | | - Suzanne M McDermott
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Nilmar Silvio Moretti
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
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143
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Ma X, Liu C, Kong X, Liu J, Zhang S, Liang S, Luan W, Cao X. Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. SCIENCE CHINA-LIFE SCIENCES 2021; 64:495-511. [DOI: 10.1007/s11427-020-1891-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
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144
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Ottenburghs J, Geng K, Suh A, Kutter C. Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds. Genome Biol Evol 2021; 13:6127176. [PMID: 33533905 PMCID: PMC8044555 DOI: 10.1093/gbe/evab016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
As a highly diverse vertebrate class, bird species have adapted to various ecological systems. How this phenotypic diversity can be explained genetically is intensively debated and is likely grounded in differences in the genome content. Larger and more complex genomes could allow for greater genetic regulation that results in more phenotypic variety. Surprisingly, avian genomes are much smaller compared to other vertebrates but contain as many protein-coding genes as other vertebrates. This supports the notion that the phenotypic diversity is largely determined by selection on non-coding gene sequences. Transfer RNAs (tRNAs) represent a group of non-coding genes. However, the characteristics of tRNA genes across bird genomes have remained largely unexplored. Here, we exhaustively investigated the evolution and functional consequences of these crucial translational regulators within bird species and across vertebrates. Our dense sampling of 55 avian genomes representing each bird order revealed an average of 169 tRNA genes with at least 31% being actively used. Unlike other vertebrates, avian tRNA genes are reduced in number and complexity but are still in line with vertebrate wobble pairing strategies and mutation-driven codon usage. Our detailed phylogenetic analyses further uncovered that new tRNA genes can emerge through multiplication by transposable elements. Together, this study provides the first comprehensive avian and cross-vertebrate tRNA gene analyses and demonstrates that tRNA gene evolution is flexible albeit constrained within functional boundaries of general mechanisms in protein translation.
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Affiliation(s)
- Jente Ottenburghs
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.,Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Sweden
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Alexander Suh
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
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145
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Zhong Q, Fu X, Zhang T, Zhou T, Yue M, Liu J, Li Z. Phylogeny and evolution of chloroplast tRNAs in Adoxaceae. Ecol Evol 2021; 11:1294-1309. [PMID: 33598131 PMCID: PMC7863635 DOI: 10.1002/ece3.7133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 11/14/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ-stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences "U-U-x2-C" and "U-x-G-x2-T," thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.
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Affiliation(s)
- Qiu‐Yi Zhong
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Xiao‐Gang Fu
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ting‐Ting Zhang
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Tong Zhou
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ming Yue
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Jian‐Ni Liu
- Department of GeologyState Key Laboratory of Continental DynamicsEarly Life InstituteNorthwest UniversityXi'anChina
| | - Zhong‐Hu Li
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
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146
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Kjærner‐Semb E, Edvardsen RB, Ayllon F, Vogelsang P, Furmanek T, Rubin CJ, Veselov AE, Nilsen TO, McCormick SD, Primmer CR, Wargelius A. Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere. Evol Appl 2021; 14:446-461. [PMID: 33664787 PMCID: PMC7896726 DOI: 10.1111/eva.13129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022] Open
Abstract
Most Atlantic salmon (Salmo salar L.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age ~10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts can help identify genetic variation related to either freshwater residency or anadromy. The objective of this study was to identify consistently divergent loci between anadromous and landlocked Atlantic salmon strains throughout their geographical distribution, with the long-term aim of identifying traits relevant for salmon aquaculture, including fresh and seawater growth, omega-3 metabolism, smoltification, and disease resistance. We used a Pool-seq approach (n = 10-40 individuals per population) to sequence the genomes of twelve anadromous and six landlocked Atlantic salmon populations covering a large part of the Northern Hemisphere and conducted a genomewide association study to identify genomic regions having been under different selection pressure in landlocked and anadromous strains. A total of 28 genomic regions were identified and included cadm1 on Chr 13 and ppargc1a on Chr 18. Seven of the regions additionally displayed consistently reduced heterozygosity in fish obtained from landlocked populations, including the genes gpr132, cdca4, and sertad2 on Chr 15. We also found 16 regions, including igf1 on Chr 17, which consistently display reduced heterozygosity in the anadromous populations compared to the freshwater populations, indicating relaxed selection on traits associated with anadromy in landlocked salmon. In conclusion, we have identified 37 regions which may harbor genetic variation relevant for improving fish welfare and quality in the salmon farming industry and for understanding life-history traits in fish.
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Affiliation(s)
| | | | | | | | | | | | - Alexey E. Veselov
- Institute of Biology of the Karelian Research CentrePetrozavodskRussia
| | - Tom Ole Nilsen
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Stephen D. McCormick
- Conte Anadromous Fish Research LaboratoryU.S. Geological Survey, Leetown Science CenterTurners FallsMAUSA
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
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147
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Luo X, Li H, Liang J, Zhao Q, Xie Y, Ren J, Zuo Z. RMVar: an updated database of functional variants involved in RNA modifications. Nucleic Acids Res 2021; 49:D1405-D1412. [PMID: 33021671 PMCID: PMC7779057 DOI: 10.1093/nar/gkaa811] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 12/30/2022] Open
Abstract
Distinguishing the few disease-related variants from a massive number of passenger variants is a major challenge. Variants affecting RNA modifications that play critical roles in many aspects of RNA metabolism have recently been linked to many human diseases, such as cancers. Evaluating the effect of genetic variants on RNA modifications will provide a new perspective for understanding the pathogenic mechanism of human diseases. Previously, we developed a database called 'm6AVar' to host variants associated with m6A, one of the most prevalent RNA modifications in eukaryotes. To host all RNA modification (RM)-associated variants, here we present an updated version of m6AVar renamed RMVar (http://rmvar.renlab.org). In this update, RMVar contains 1 678 126 RM-associated variants for 9 kinds of RNA modifications, namely m6A, m6Am, m1A, pseudouridine, m5C, m5U, 2'-O-Me, A-to-I and m7G, at three confidence levels. Moreover, RBP binding regions, miRNA targets, splicing events and circRNAs were integrated to assist investigations of the effects of RM-associated variants on posttranscriptional regulation. In addition, disease-related information was integrated from ClinVar and other genome-wide association studies (GWAS) to investigate the relationship between RM-associated variants and diseases. We expect that RMVar may boost further functional studies on genetic variants affecting RNA modifications.
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Affiliation(s)
- Xiaotong Luo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Huiqin Li
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiaqi Liang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Yubin Xie
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
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148
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Rauscher R, Bampi GB, Guevara-Ferrer M, Santos LA, Joshi D, Mark D, Strug LJ, Rommens JM, Ballmann M, Sorscher EJ, Oliver KE, Ignatova Z. Positive epistasis between disease-causing missense mutations and silent polymorphism with effect on mRNA translation velocity. Proc Natl Acad Sci U S A 2021; 118:e2010612118. [PMID: 33468668 PMCID: PMC7848603 DOI: 10.1073/pnas.2010612118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Epistasis refers to the dependence of a mutation on other mutation(s) and the genetic context in general. In the context of human disorders, epistasis complicates the spectrum of disease symptoms and has been proposed as a major contributor to variations in disease outcome. The nonadditive relationship between mutations and the lack of complete understanding of the underlying physiological effects limit our ability to predict phenotypic outcome. Here, we report positive epistasis between intragenic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR)-the gene responsible for cystic fibrosis (CF) pathology. We identified a synonymous single-nucleotide polymorphism (sSNP) that is invariant for the CFTR amino acid sequence but inverts translation speed at the affected codon. This sSNP in cis exhibits positive epistatic effects on some CF disease-causing missense mutations. Individually, both mutations alter CFTR structure and function, yet when combined, they lead to enhanced protein expression and activity. The most robust effect was observed when the sSNP was present in combination with missense mutations that, along with the primary amino acid change, also alter the speed of translation at the affected codon. Functional studies revealed that synergistic alteration in ribosomal velocity is the underlying mechanism; alteration of translation speed likely increases the time window for establishing crucial domain-domain interactions that are otherwise perturbed by each individual mutation.
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Affiliation(s)
- Robert Rauscher
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Giovana B Bampi
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Marta Guevara-Ferrer
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Leonardo A Santos
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
- Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - David Mark
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Lisa J Strug
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Department of Statistical Sciences, Computer Science and Division of Biostatistics, University of Toronto, Toronto M5G 0A4, Canada
| | - Johanna M Rommens
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto M5G 0A4, Canada
| | | | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
- Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Kathryn E Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
- Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Zoya Ignatova
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany;
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149
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Liu Y, Chen Y. Mitochondrial tRNA Mutations Associated With Essential Hypertension: From Molecular Genetics to Function. Front Cell Dev Biol 2021; 8:634137. [PMID: 33585472 PMCID: PMC7874112 DOI: 10.3389/fcell.2020.634137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Essential hypertension (EH) is one of the most common cardiovascular diseases worldwide, entailing a high level of morbidity. EH is a multifactorial disease influenced by both genetic and environmental factors, including mitochondrial DNA (mtDNA) genotype. Previous studies identified mtDNA mutations that are associated with maternally inherited hypertension, including tRNAIle m.4263A>G, m.4291T>C, m.4295A>G, tRNAMet m.4435A>G, tRNAAla m.5655A>G, and tRNAMet/tRNAGln m.4401A>G, et al. These mtDNA mutations alter tRNA structure, thereby leading to metabolic disorders. Metabolic defects associated with mitochondrial tRNAs affect protein synthesis, cause oxidative phosphorylation defects, reduced ATP synthesis, and increase production of reactive oxygen species. In this review we discuss known mutations of tRNA genes encoded by mtDNA and the potential mechanisms by which these mutations may contribute to hypertension.
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Affiliation(s)
- Yuqi Liu
- Cardiac Department, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Department of Cardiology & National Clinical Research Center of Geriatrics Disease, Chinese PLA General Hospital, Beijing, China.,Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China.,National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yundai Chen
- Cardiac Department, Chinese PLA General Hospital, Beijing, China
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150
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Termathe M, Leidel SA. Urm1: A Non-Canonical UBL. Biomolecules 2021; 11:biom11020139. [PMID: 33499055 PMCID: PMC7911844 DOI: 10.3390/biom11020139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/10/2023] Open
Abstract
Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RHD). This sulfurtransferase domain catalyzes the formation of a C-terminal thiocarboxylate on Urm1. Thiocarboxylated Urm1 is the sulfur donor for 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a chemical nucleotide modification at the wobble position in tRNA. This thio-modification is conserved in all domains of life and optimizes translation. The absence of Urm1 increases stress sensitivity in yeast triggered by defects in protein homeostasis, a hallmark of neurological defects in higher organisms. In contrast, elevated levels of tRNA modifying enzymes promote the appearance of certain types of cancer and the formation of metastasis. Here, we summarize recent findings on the unique features that place Urm1 at the intersection of UBL and SCP and make Urm1 an excellent model for studying the evolution of protein conjugation and sulfur-carrier systems.
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Affiliation(s)
- Martin Termathe
- Institute of Biochemistry, Protein Biochemistry and Photobiocatalysis, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany;
| | - Sebastian A. Leidel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Correspondence:
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