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Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
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Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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2
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Li J, Kang X, Guidi I, Lu L, Fernández-Millán P, Prats-Ejarque G, Boix E. Structural determinants for tRNA selective cleavage by RNase 2/EDN. Structure 2024; 32:328-341.e4. [PMID: 38228145 DOI: 10.1016/j.str.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
tRNA-derived fragments (tRFs) have emerged as key players of immunoregulation. Some RNase A superfamily members participate in the shaping of the tRFs population. By comparing wild-type and knockout macrophage cell lines, our previous work revealed that RNase 2 can selectively cleave tRNAs. Here, we confirm the in vitro protein cleavage pattern by screening of synthetic tRNAs, single-mutant variants, and anticodon-loop DNA/RNA hairpins. By sequencing of tRF products, we identified the cleavage selectivity of recombinant RNase 2 with base specificity at B1 (U/C) and B2 (A) sites, consistent with a previous cellular study. Lastly, protein-hairpin complexes were predicted by MD simulations. Results reveal the contribution of the α1, loop 3 and loop 4, and β6 RNase 2 regions, where residues Arg36/Asn39/Gln40/Asn65/Arg68/Arg132 provide interactions, spanning from P-1 to P2 sites that are essential for anticodon loop recognition. Knowledge of RNase 2-specific tRFs generation might guide new therapeutic approaches for infectious and immune-related diseases.
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Affiliation(s)
- Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Xincheng Kang
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Irene Guidi
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Pablo Fernández-Millán
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain.
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Rashad S, Al-Mesitef S, Mousa A, Zhou Y, Ando D, Sun G, Fukuuchi T, Iwasaki Y, Xiang J, Byrne SR, Sun J, Maekawa M, Saigusa D, Begley TJ, Dedon PC, Niizuma K. Translational response to mitochondrial stresses is orchestrated by tRNA modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580389. [PMID: 38405984 PMCID: PMC10888749 DOI: 10.1101/2024.02.14.580389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitochondrial stress and dysfunction play important roles in many pathologies. However, how cells respond to mitochondrial stress is not fully understood. Here, we examined the translational response to electron transport chain (ETC) inhibition and arsenite induced mitochondrial stresses. Our analysis revealed that during mitochondrial stress, tRNA modifications (namely f5C, hm5C, queuosine and its derivatives, and mcm5U) dynamically change to fine tune codon decoding, usage, and optimality. These changes in codon optimality drive the translation of many pathways and gene sets, such as the ATF4 pathway and selenoproteins, involved in the cellular response to mitochondrial stress. We further examined several of these modifications using targeted approaches. ALKBH1 knockout (KO) abrogated f5C and hm5C levels and led to mitochondrial dysfunction, reduced proliferation, and impacted mRNA translation rates. Our analysis revealed that tRNA queuosine (tRNA-Q) is a master regulator of the mitochondrial stress response. KO of QTRT1 or QTRT2, the enzymes responsible for tRNA-Q synthesis, led to mitochondrial dysfunction, translational dysregulation, and metabolic alterations in mitochondria-related pathways, without altering cellular proliferation. In addition, our analysis revealed that tRNA-Q loss led to a domino effect on various tRNA modifications. Some of these changes could be explained by metabolic profiling. Our analysis also revealed that utilizing serum deprivation or alteration with Queuine supplementation to study tRNA-Q or stress response can introduce various confounding factors by altering many other tRNA modifications. In summary, our data show that tRNA modifications are master regulators of the mitochondrial stress response by driving changes in codon decoding.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shadi Al-Mesitef
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Abdulrahman Mousa
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuan Zhou
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daisuke Ando
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurology, Tohoku university Graduate school of Medicine, Sendai, Japan
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Tomoko Fukuuchi
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yuko Iwasaki
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Jingdong Xiang
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Codomax Inc, 17 Briden St STE 219, Worcester, MA 01605
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, Albany, NY, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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Motorin Y, Helm M. General Principles and Limitations for Detection of RNA Modifications by Sequencing. Acc Chem Res 2024; 57:275-288. [PMID: 38065564 PMCID: PMC10851944 DOI: 10.1021/acs.accounts.3c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 02/07/2024]
Abstract
Among the many analytical methods applied to RNA modifications, a particularly pronounced surge has occurred in the past decade in the field of modification mapping. The occurrence of modifications such as m6A in mRNA, albeit known since the 1980s, became amenable to transcriptome-wide analyses through the advent of next-generation sequencing techniques in a rather sudden manner. The term "mapping" here refers to detection of RNA modifications in a sequence context, which has a dramatic impact on the interpretation of biological functions. As a consequence, an impressive number of mapping techniques were published, most in the perspective of what now has become known as "epitranscriptomics". While more and more different modifications were reported to occur in mRNA, conflicting reports and controversial results pointed to a number of technical and theoretical problems rooted in analytics, statistics, and reagents. Rather than finding the proverbial needle in a haystack, the tasks were to determine how many needles of what color in what size of a haystack one was looking at.As the authors of this Account, we think it important to outline the limitations of different mapping methods since many life scientists freshly entering the field confuse the accuracy and precision of modification mapping with that of normal sequencing, which already features numerous caveats by itself. Indeed, we propose here to qualify a specific mapping method by the size of the transcriptome that can be meaningfully analyzed with it.We here focus on high throughput sequencing by Illumina technology, referred to as RNA-Seq. We noted with interest the development of methods for modification detection by other high throughput sequencing platforms that act directly on RNA, e.g., PacBio SMRT and nanopore sequencing, but those are not considered here.In contrast to approaches relying on direct RNA sequencing, current Illumina RNA-Seq protocols require prior conversion of RNA into DNA. This conversion relies on reverse transcription (RT) to create cDNA; thereafter, the cDNA undergoes a sequencing-by-synthesis type of analysis. Thus, a particular behavior of RNA modified nucleotides during the RT-step is a prerequisite for their detection (and quantification) by deep sequencing, and RT properties have great influence on the detection efficiency and reliability. Moreover, the RT-step requires annealing of a synthetic primer, a prerequisite with a crucial impact on library preparation. Thus, all RNA-Seq protocols must feature steps for the introduction of primers, primer landing sites, or adapters on both the RNA 3'- and 5'-ends.
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Affiliation(s)
- Yuri Motorin
- Université
de Lorraine, UMR7365 IMoPA CNRS-UL
and UAR2008/US40 IBSLor CNRS-Inserm, Biopole UL, Nancy F54000, France
| | - Mark Helm
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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Wu F, Yang Q, Pan W, Meng W, Ma Z, Wang W. tRNA-derived fragments: mechanism of gene regulation and clinical application in lung cancer. Cell Oncol (Dordr) 2024; 47:37-54. [PMID: 37642916 DOI: 10.1007/s13402-023-00864-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Lung cancer, being the most widespread and lethal form of cancer globally, has a high incidence and mortality rate primarily attributed to challenges associated with early detection, extensive metastasis, and frequent recurrence. In the context of lung cancer development, noncoding RNA molecules have a crucial role in governing gene expression and protein synthesis. Specifically, tRNA-derived fragments (tRFs), a subset of noncoding RNAs, exert significant biological influences on cancer progression, encompassing transcription and translation processes as well as epigenetic regulation. This article primarily examines the mechanisms by which tRFs modulate gene expression and contribute to tumorigenesis in lung cancer. Furthermore, we provide a comprehensive overview of the current bioinformatics analysis of tRFs in lung cancer, with the objective of offering a systematic and efficient approach for studying the expression profiling, functional enrichment, and molecular mechanisms of tRFs in this disease. Finally, we discuss the clinical significance and potential avenues for future research on tRFs in lung cancer. This paper presents a comprehensive systematic review of the existing research findings on tRFs in lung cancer, aiming to offer improved biomarkers and drug targets for clinical management of lung cancer.
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Affiliation(s)
- Fan Wu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Qianqian Yang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Wei Meng
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Zhongliang Ma
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China.
| | - Weiwei Wang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Cancer Hospital, Yunnan Cancer Center, Kunming, 650118, China.
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Du J, Huang T, Zheng Z, Fang S, Deng H, Liu K. Biological function and clinical application prospect of tsRNAs in digestive system biology and pathology. Cell Commun Signal 2023; 21:302. [PMID: 37904174 PMCID: PMC10614346 DOI: 10.1186/s12964-023-01341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023] Open
Abstract
tsRNAs are small non-coding RNAs originating from tRNA that play important roles in a variety of physiological activities such as RNA silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, as well as involvement in cellular differentiation, proliferation, and apoptosis. tsRNA-related abnormalities have a significant influence on the onset, development, and progression of numerous human diseases, including malignant tumors through affecting the cell cycle and specific signaling molecules. This review introduced origins together with tsRNAs classification, providing a summary for regulatory mechanism and physiological function while dysfunctional effect of tsRNAs in digestive system diseases, focusing on the clinical prospects of tsRNAs for diagnostic and prognostic biomarkers. Video Abstract.
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Affiliation(s)
- Juan Du
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Tianyi Huang
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Zhen Zheng
- Department of Radiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Shuai Fang
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Hongxia Deng
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Kaitai Liu
- Department of Radiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
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Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
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Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
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