1
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Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
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Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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2
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Xiong QP, Li J, Li H, Huang ZX, Dong H, Wang ED, Liu RJ. Human TRMT1 catalyzes m 2G or m 22G formation on tRNAs in a substrate-dependent manner. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2295-2309. [PMID: 37204604 DOI: 10.1007/s11427-022-2295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/30/2023] [Indexed: 05/20/2023]
Abstract
TRMT1 is an N2-methylguanosine (m2G) and N2,N2-methylguanosine (m22G) methyltransferase that targets G26 of both cytoplasmic and mitochondrial tRNAs. In higher eukaryotes, most cytoplasmic tRNAs with G26 carry m22G26, although the majority of mitochondrial G26-containing tRNAs carry m2G26 or G26, suggesting differences in the mechanisms by which TRMT1 catalyzes modification of these tRNAs. Loss-of-function mutations of human TRMT1 result in neurological disorders and completely abrogate tRNA:m22G26 formation. However, the mechanism underlying the independent catalytic activity of human TRMT1 and identity of its specific substrate remain elusive, hindering a comprehensive understanding of the pathogenesis of neurological disorders caused by TRMT1 mutations. Here, we showed that human TRMT1 independently catalyzes formation of the tRNA:m2G26 or m22G26 modification in a substrate-dependent manner, which explains the distinct distribution of m2G26 and m22G26 on cytoplasmic and mitochondrial tRNAs. For human TRMT1-mediated tRNA:m22G26 formation, the semi-conserved C11:G24 serves as the determinant, and the U10:A25 or G10:C25 base pair is also required, while the size of the variable loop has no effect. We defined the requirements of this recognition mechanism as the "m22G26 criteria". We found that the m22G26 modification occurred in almost all the higher eukaryotic tRNAs conforming to these criteria, suggesting the "m22G26 criteria" are applicable to other higher eukaryotic tRNAs.
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Affiliation(s)
- Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhi-Xuan Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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3
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Funk HM, Zhao R, Thomas M, Spigelmyer SM, Sebree NJ, Bales RO, Burchett JB, Mamaril JB, Limbach PA, Guy MP. Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants. PLoS One 2020; 15:e0242737. [PMID: 33253256 PMCID: PMC7704012 DOI: 10.1371/journal.pone.0242737] [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: 04/02/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Posttranscriptional modification of tRNA is critical for efficient protein translation and proper cell growth, and defects in tRNA modifications are often associated with human disease. Although most of the enzymes required for eukaryotic tRNA modifications are known, many of these enzymes have not been identified and characterized in several model multicellular eukaryotes. Here, we present two related approaches to identify the genes required for tRNA modifications in multicellular organisms using primer extension assays with fluorescent oligonucleotides. To demonstrate the utility of these approaches we first use expression of exogenous genes in yeast to experimentally identify two TRM1 orthologs capable of forming N2,N2-dimethylguanosine (m2,2G) on residue 26 of cytosolic tRNA in the model plant Arabidopsis thaliana. We also show that a predicted catalytic aspartate residue is required for function in each of the proteins. We next use RNA interference in cultured Drosophila melanogaster cells to identify the gene required for m2,2G26 formation on cytosolic tRNA. Additionally, using these approaches we experimentally identify D. melanogaster gene CG10050 as the corresponding ortholog of human DTWD2, which encodes the protein required for formation of 3-amino-3-propylcarboxyuridine (acp3U) on residue 20a of cytosolic tRNA. We further show that A. thaliana gene AT2G41750 can form acp3U20b on an A. thaliana tRNA expressed in yeast cells, and that the aspartate and tryptophan residues in the DXTW motif of this protein are required for modification activity. These results demonstrate that these approaches can be used to study tRNA modification enzymes.
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Affiliation(s)
- Holly M. Funk
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Maggie Thomas
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Sarah M. Spigelmyer
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Nichlas J. Sebree
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Regan O. Bales
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Jamison B. Burchett
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Justen B. Mamaril
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Michael P. Guy
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
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4
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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5
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Fandilolu P, Kamble AS, Dound AS, Sonawane KD. Role of Wybutosine and Mg 2+ Ions in Modulating the Structure and Function of tRNA Phe: A Molecular Dynamics Study. ACS OMEGA 2019; 4:21327-21339. [PMID: 31867527 PMCID: PMC6921629 DOI: 10.1021/acsomega.9b02238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
Transfer RNA remains to be a mysterious molecule of the cell repertoire. With its modified bases and selectivity of codon recognition, it remains to be flexible inside the ribosomal machinery for smooth and hassle-free protein biosynthesis. Structural changes occurring in tRNA due to the presence or absence of wybutosine, with and without Mg2+ ions, have remained a point of interest for structural biologists. Very few studies have come to a conclusion correlating the changes either with the structure and flexibility or with the codon recognition. Considering the above facts, we have implemented molecular modeling methods to address these problems using multiple molecular dynamics (MD) simulations of tRNAPhe along with codons. Our results highlight some of the earlier findings and also shed light on some novel structural and functional aspects. Changes in the stability of tRNAPhe in native or codon-bound states result from the conformations of constituent nucleotides with respect to each other. A smaller change in their conformations leads to structural distortions in the base-pairing geometry and eventually in the ribose-phosphate backbone. MD simulation studies highlight the preference of UUC codons over UUU by tRNAPhe in the presence of wybutosine and Mg2+ ions. This study also suggests that magnesium ions are required by tRNAPhe for proper recognition of UUC/UUU codons during ribosomal interactions with tRNA.
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Affiliation(s)
- Prayagraj
M. Fandilolu
- Structural
Bioinformatics Unit, Department of Biochemistry and Department of
Microbiology, Shivaji University, Kolhapur 416004, Maharashtra, India
| | - Asmita S. Kamble
- Structural
Bioinformatics Unit, Department of Biochemistry and Department of
Microbiology, Shivaji University, Kolhapur 416004, Maharashtra, India
| | - Ambika S. Dound
- Structural
Bioinformatics Unit, Department of Biochemistry and Department of
Microbiology, Shivaji University, Kolhapur 416004, Maharashtra, India
| | - Kailas D. Sonawane
- Structural
Bioinformatics Unit, Department of Biochemistry and Department of
Microbiology, Shivaji University, Kolhapur 416004, Maharashtra, India
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6
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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7
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Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D. TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Mol Cell Biol 2017; 37:e00214-17. [PMID: 28784718 PMCID: PMC5640816 DOI: 10.1128/mcb.00214-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/17/2017] [Accepted: 07/29/2017] [Indexed: 02/07/2023] Open
Abstract
Mutations in the tRNA methyltransferase 1 (TRMT1) gene have been identified as the cause of certain forms of autosomal-recessive intellectual disability (ID). However, the molecular pathology underlying ID-associated TRMT1 mutations is unknown, since the biological role of the encoded TRMT1 protein remains to be determined. Here, we have elucidated the molecular targets and function of TRMT1 to uncover the cellular effects of ID-causing TRMT1 mutations. Using human cells that have been rendered deficient in TRMT1, we show that TRMT1 is responsible for catalyzing the dimethylguanosine (m2,2G) base modification in both nucleus- and mitochondrion-encoded tRNAs. TRMT1-deficient cells exhibit decreased proliferation rates, alterations in global protein synthesis, and perturbations in redox homeostasis, including increased endogenous ROS levels and hypersensitivity to oxidizing agents. Notably, ID-causing TRMT1 variants are unable to catalyze the formation of m2,2G due to defects in RNA binding and cannot rescue oxidative stress sensitivity. Our results uncover a biological role for TRMT1-catalyzed tRNA modification in redox metabolism and show that individuals with TRMT1-associated ID are likely to have major perturbations in cellular homeostasis due to the lack of m2,2G modifications.
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Affiliation(s)
- Joshua M Dewe
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Benjamin L Fuller
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | | | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
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8
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Fandilolu PM, Kamble AS, Sambhare SB, Sonawane KD. Conformational preferences and structural analysis of hypermodified nucleoside, peroxywybutosine (o2yW) found at 37 th position in anticodon loop of tRNA Phe and its role in modulating UUC codon-anticodon interactions. Gene 2017; 641:310-325. [PMID: 29107006 DOI: 10.1016/j.gene.2017.10.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 09/02/2017] [Accepted: 10/25/2017] [Indexed: 12/17/2022]
Abstract
Hypermodified bases present at 3'-adjacent (37th) position in anticodon loop of tRNAPhe are well known for their contribution in modulating codon-anticodon interactions. Peroxywybutosine (o2yW), a wyosine family member, is one of such tricyclic modified bases observed at the 37th position in tRNAPhe. Conformational preferences and three-dimensional structural analysis of peroxywybutosine have not been investigated in detail at atomic level. Hence, in the present study quantum chemical semi-empirical RM1 and multiple molecular dynamics (MD) simulations have been used to study structural significance of peroxywybutosine in tRNAPhe. Full geometry optimizations over the peroxywybutosine base have also been performed using ab-initio HF-SCF (6-31G**), DFT (B3LYP/6-31G**) and semi-empirical PM6 method to compare the salient properties. RM1 predicted most stable structure shows that the amino-carboxy-propyl side chain of o2yW remains 'distal' to the five membered imidazole ring of tricyclic guanosine. MD simulation trajectory of the isolated peroxy base showed restricted periodical fluctuations of peroxywybutosine side chain which might be helpful to maintain proper anticodon loop structure and mRNA reading frame during protein biosynthesis process. Another comparative MD simulation study of the anticodon stem loop with codon UUC showed various properties, which justify the functional implications of peroxywybutosine at 37th position along with other modified bases present in ASL of tRNAPhe. Thus, this study presents an atomic view into the structural properties of peroxywybutosine, which can be useful to determine its role in the anticodon stem loop in context of codon-anticodon interactions and frame shift mutations.
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Affiliation(s)
- Prayagraj M Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra (M.S.), India
| | - Asmita S Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra (M.S.), India
| | - Susmit B Sambhare
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra (M.S.), India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra (M.S.), India; Department of Microbiology, Shivaji University, Kolhapur, 416004, Maharashtra (MS), India.
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9
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Stojković V, Fujimori DG. Mutations in RNA methylating enzymes in disease. Curr Opin Chem Biol 2017; 41:20-27. [PMID: 29059606 DOI: 10.1016/j.cbpa.2017.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/06/2023]
Abstract
RNA methylation is an abundant modification identified in various RNA species in both prokaryotic and eukaryotic organisms. However, the functional roles for the majority of these methylations remain largely unclear. In eukaryotes, many RNA methylations have been suggested to participate in fundamental cellular processes. Mutations in eukaryotic RNA methylating enzymes, and a consequent change in methylation, can lead to the development of diseases and disorders. In contrast, loss of RNA methylation in prokaryotes can be beneficial to microorganisms, especially under antibiotic pressure. Here we discuss several recent advances in understanding mutational landscape of both eukaryotic and prokaryotic RNA methylating enzymes and their relevance to disease and antibiotic resistance.
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Affiliation(s)
- Vanja Stojković
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States.
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10
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Conformational Preferences of Modified Nucleoside 5-Taurinomethyluridine, τm(5)U Occur at 'wobble' 34th Position in the Anticodon Loop of tRNA. Cell Biochem Biophys 2016; 71:1589-603. [PMID: 25388845 DOI: 10.1007/s12013-014-0382-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Conformational preferences of hypermodified nucleoside 5-taurinomethyluridine 5'-monophoshate 'p-τm(5)U' (-CH2-NH2(+)-CH2-CH2-SO3(-)) have been investigated using semi-empirical RM1 method. Automated geometry optimization using ab initio molecular orbital HF-SCF (6-31G**) and DFT (B3LYP/6-31G**) calculations have also been made to compare the salient features. The RM1 preferred most stable conformation of 'p-τm(5)U' has been stabilized by hydrogen bonding interactions between O(11a)…HN(8), O1P(34)…HN(8), and O1P(34)…HC(10). Another conformational study of 5-taurinomethyluridine side chain has also been performed in context of anticodon loop bases of E. coli tRNA(Leu). The atom O(11a) of τm(5)U(34) side chain interacts with adenosine (A35) as well as ribose-phosphate backbone which might provide structural stability to the anticodon loop. The glycosyl torsion angle of τm(5)U retains 'anti'-conformation. The solvent accessible surface area calculations revealed the role of τm(5)U in tRNA(Leu) anticodon loop. MD simulation results are found in agreement with RM1 preferred stable structure. The MEPs calculations of τm(5)U(34):G3 model show unique potential tunnels between the hydrogen bond donor and acceptor atoms as compared to τm(5)U(34):A3 model. Thus, these results could pave the way to understand the role of τm(5)U(34) to recognize UUG/UUA codons at atomic level in the mitochondrial disease, MELAS.
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11
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Sonawane KD, Sambhare SB. The influence of hypermodified nucleosides lysidine and t(6)A to recognize the AUA codon instead of AUG: a molecular dynamics simulation study. Integr Biol (Camb) 2016. [PMID: 26215455 DOI: 10.1039/c5ib00058k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hypermodified nucleosides lysidine (L) and N(6)-threonylcarbamoyladenosine (t(6)A) influence codon-anticodon interactions during the protein biosynthesis process. Lysidine prevents the misrecognition of the AUG codon as isoleucine and that of AUA as methionine. The structural significance of these modified bases has not been studied in detail at the atomic level. Hence, in the present study we performed multiple molecular dynamics (MD) simulations of anticodon stem loop (ASL) of tRNA(Ile) in the presence and absence of modified bases 'L' and 't(6)A' at the 34th and 37th positions respectively along with trinucleotide 'AUA' and 'AUG' codons. Hydrogen bonding interactions formed by the tautomeric form of lysidine may assist in reading the third base adenine of the 'AUA' codon, unlike the guanine of the 'AUG' codon. Such interactions might be useful to restrict codon specificity to recognize isoleucine tRNA instead of methionine tRNA. The t(6)A side chain interacts with the purine ring of the first codon nucleotide adenine, which might provide base stacking interactions and could be responsible for restricting extended codon-anticodon recognition. We found that ASL tRNA(Ile) in the absence of modifications at the 34th and 37th positions cannot establish proper hydrogen bonding interactions to recognize the isoleucine codon 'AUA' and subsequently disturbs the anticodon loop structure. The binding free energy calculations revealed that tRNA(Ile) ASL with modified nucleosides prefers the codon AUA over AUG. Thus, these findings might be useful to understand the role of modified bases L and t(6)A to recognize the AUA codon instead of AUG.
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Affiliation(s)
- Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur-416 004, Maharashtra, India. and Department of Microbiology, Shivaji University, Kolhapur- 416 004, Maharashtra, India
| | - Susmit B Sambhare
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur-416 004, Maharashtra, India.
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12
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Comparative Structural Dynamics of tRNA(Phe) with Respect to Hinge Region Methylated Guanosine: A Computational Approach. Cell Biochem Biophys 2016; 74:157-73. [PMID: 27216172 DOI: 10.1007/s12013-016-0731-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/01/2016] [Indexed: 12/13/2022]
Abstract
Transfer RNAs (tRNAs) contain various uniquely modified nucleosides thought to be useful for maintaining the structural stability of tRNAs. However, their significance for upholding the tRNA structure has not been investigated in detail at the atomic level. In this study, molecular dynamic simulations have been performed to assess the effects of methylated nucleic acid bases, N (2)-methylguanosine (m(2)G) and N (2)-N (2)-dimethylguanosine (m 2 (2) G) at position 26, i.e., the hinge region of E. coli tRNA(Phe) on its structure and dynamics. The results revealed that tRNA(Phe) having unmodified guanosine in the hinge region (G26) shows structural rearrangement in the core of the molecule, resulting in lack of base stacking interactions, U-turn feature of the anticodon loop, and TΨC loop. We show that in the presence of the unmodified guanosine, the overall fold of tRNA(Phe) is essentially not the same as that of m(2)G26 and m 2 (2) G26 containing tRNA(Phe). This structural rearrangement arises due to intrinsic factors associated with the weak hydrogen-bonding patterns observed in the base triples of the tRNA(Phe) molecule. The m(2)G26 and m 2 (2) G26 containing tRNA(Phe) retain proper three-dimensional fold through tertiary interactions. Single-point energy and molecular electrostatics potential calculation studies confirmed the structural significance of tRNAs containing m(2)G26 and m 2 (2) G26 compared to tRNA with normal G26, showing that the mono-methylated (m(2)G26) and dimethylated (m 2 (2) G26) modifications are required to provide structural stability not only in the hinge region but also in the other parts of tRNA(Phe). Thus, the present study allows us to better understand the effects of modified nucleosides and ionic environment on tRNA folding.
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13
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Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U, found at ‘wobble’ position in anticodon loop of human mitochondrial tRNALys. Struct Chem 2015. [DOI: 10.1007/s11224-015-0642-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Daghir-Wojtkowiak E, Struck-Lewicka W, Waszczuk-Jankowska M, Markuszewski M, Kaliszan R, Markuszewski MJ. Statistical-based approach in potential diagnostic application of urinary nucleosides in urogenital tract cancer. Biomark Med 2015; 9:577-95. [DOI: 10.2217/bmm.15.20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: We aimed at evaluation the potential diagnostic role of urinary nucleosides in urogenital tract cancer. Materials & methods: Concentrations of 12 nucleosides determined by LC-MS/MS were subjected to correlation, association and interaction analyses. Results: We identified six pairs of nucleosides differently correlated in the group of patients and controls (p < 0.05). N-2-methylguanosine (odds ratio: 4.82; 95% CI: 1.78–12.93; p = 0.002) and N,N-dimethylguanosine (odds ratio: 5.45; 95% CI: 1.78–16.44; p = 0.003), were significantly associated with the disease risk (p-corrected = 0.004). Interaction between N-2-methylguanosine and adenosine (p-interaction = 0.019) suggested their multiplicative effect on the outcome. Conclusion: Urinary nucleosides, namely N,N-dimethylguanosine and N-2-methylguanosine may have the potential to serve as prognostic biomarkers. Gender-specific differences in urogenital tract cancer are likely to occur.
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Affiliation(s)
- Emilia Daghir-Wojtkowiak
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
- Department of Toxicology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, M. Curie-Sklodowskiej 9, 85-094 Bydgoszcz, Poland
| | - Wiktoria Struck-Lewicka
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Malgorzata Waszczuk-Jankowska
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Marcin Markuszewski
- Department of Urology, Medical University of Gdańsk, Smoluchowskiego 17, 80–214 Gdańsk, Poland
| | - Roman Kaliszan
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Michal Jan Markuszewski
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
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Conformational preferences of modified nucleoside N(4)-acetylcytidine, ac4C occur at "wobble" 34th position in the anticodon loop of tRNA. Cell Biochem Biophys 2014; 66:797-816. [PMID: 23408308 DOI: 10.1007/s12013-013-9525-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Conformational preferences of modified nucleoside, N(4)-acetylcytidine, ac(4)C have been investigated using quantum chemical semi-empirical RM1 method. Automated geometry optimization using PM3 method along with ab initio methods HF SCF (6-31G**), and density functional theory (DFT; B3LYP/6-31G**) have also been made to compare the salient features. The most stable conformation of N(4)-acetyl group of ac(4)C prefers "proximal" orientation. This conformation is stabilized by intramolecular hydrogen bonding between O(7)···HC(5), O(2)···HC2', and O4'···HC(6). The "proximal" conformation of N(4)-acetyl group has also been observed in another conformational study of anticodon loop of E. coli elongator tRNA(Met). The solvent accessible surface area (SASA) calculations revealed the role of ac(4)C in anticodon loop. The explicit molecular dynamics simulation study also shows the "proximal" orientation of N(4)-acetyl group. The predicted "proximal" conformation would allow ac(4)C to interact with third base of codon AUG/AUA whereas the 'distal' orientation of N(4)-acetyl cytidine side-chain prevents such interactions. Single point energy calculation studies of various models of anticodon-codon bases revealed that the models ac(4)C(34)(Proximal):G3, and ac(4)C(34)(Proximal):A3 are energetically more stable as compared to models ac(4)C(34)(Distal):G3, and ac(4)C(34)(Distal):A3, respectively. MEPs calculations showed the unique potential tunnels between the hydrogen bond donor-acceptor atoms of ac(4)C(34)(Proximal):G3/A3 base pairs suggesting role of ac(4)C in recognition of third letter of codons AUG/AUA. The "distal" conformation of ac(4)C might prevent misreading of AUA codon. Hence, this study could be useful to understand the role of ac(4)C in the tertiary structure folding of tRNA as well as in the proper recognition of codons during protein biosynthesis process.
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Sambhare SB, Kumbhar BV, Kamble AD, Bavi RS, Kumbhar NM, Sonawane KD. Structural significance of modified nucleosides k2C and t6A present in the anticodon loop of tRNAIle. RSC Adv 2014. [DOI: 10.1039/c3ra47335j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Bavi RS, Sambhare SB, Sonawane KD. MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m(2)G and m(2) 2G present in tRNA. Comput Struct Biotechnol J 2013; 5:e201302015. [PMID: 24688708 PMCID: PMC3962230 DOI: 10.5936/csbj.201302015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/16/2013] [Accepted: 05/19/2013] [Indexed: 11/28/2022] Open
Abstract
Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G) is the second most often encountered nucleoside in E. coli tRNAs. N2, N2- dimethylguanosine (m22G) is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.
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Affiliation(s)
- Rohit S Bavi
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416 004, Maharashtra, India
| | - Susmit B Sambhare
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416 004, Maharashtra, India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416 004, Maharashtra, India ; Department of Microbiology, Shivaji University, Kolhapur 416 004, Maharashtra, India
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Kumbhar NM, Kumbhar BV, Sonawane KD. Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNA(Phe). J Mol Graph Model 2012; 38:174-85. [PMID: 23073221 DOI: 10.1016/j.jmgm.2012.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNA(Phe). The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers 'distal' conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson-Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the 'distal' orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).
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Affiliation(s)
- Navanath M Kumbhar
- Department of Biotechnology, Shivaji University, Kolhapur 416004, Maharashtra-MS, India
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