1
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Li H, Liu H, Zhu D, Dou C, Gang B, Zhang M, Wan Z. Biological function molecular pathways and druggability of DNMT2/TRDMT1. Pharmacol Res 2024; 205:107222. [PMID: 38782147 DOI: 10.1016/j.phrs.2024.107222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
5-methylcytosine (m5C) is among the most common epigenetic modification in DNA and RNA molecules, and plays an important role in the animal development and disease pathogenesis. Interestingly, unlike other m5C DNA methyltransferases (DNMTs), DNMT2/TRDMT1 has the double-substrate specificity and adopts a DNMT-similar catalytic mechanism to methylate RNA. Moreover, it is widely involved in a variety of physiological regulatory processes, such as the gene expression, precise protein synthesis, immune response, and disease occurrence. Thus, comprehending the epigenetic mechanism and function of DNMT2/TRDMT1 will probably provide new strategies to treat some refractory diseases. Here, we discuss recent studies on the spatiotemporal expression pattern and post-translational modifications of DNMT2/TRDMT1, and summarize the research advances in substrate characteristics, catalytic recognition mechanism, DNMT2/TRDMT1-related genes or proteins, pharmacological application, and inhibitor development. This review will shed light on the pharmacological design by targeting DNMT2/TRDMT1 to treat parasitic, viral and oncologic diseases.
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Affiliation(s)
- Huari Li
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China; College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei Province 430070, PR China.
| | - Huiru Liu
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei Province 430070, PR China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Chengli Dou
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Baocai Gang
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Mengjie Zhang
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Ziyu Wan
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
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2
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Li H, Zhu D, Yang Y, Ma Y, Chen Y, Xue P, Chen J, Qin M, Xu D, Cai C, Cheng H. Restricted tRNA methylation by intermolecular disulfide bonds in DNMT2/TRDMT1. Int J Biol Macromol 2023; 251:126310. [PMID: 37579906 DOI: 10.1016/j.ijbiomac.2023.126310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Reportedly, DNMT2/TRDMT1 mainly methylates tRNAs at C38 and prevents them from the cleavage under stress. It also plays an essential role in the survival and physiological homeostasis of organisms. Nevertheless, DNMT2/TRDMT1 exhibits much weaker tRNA methylation activity in vitro than other tRNA methyltransferases, TrmD and Trm5. Here, we explored the restricted tRNA methylation mechanism by DNMT2/TRDMT1. In the current study, the optimized buffer C at 37 °C was the best condition for DNMT2/TRDMT1 activation. Of note, Dithiothreitol (DTT) was an indispensable component for this enzyme catalysis. Moreover, reductants took similar effects on the conformation change and oligomeric formation of DNMT2/TRDMT1. Ultimately, LC-MS/MS result revealed that C292-C292 and C292-C287 were predominant intermolecular disulfide bonds in recombinant DNMT2/TRDMT1. Notably, DNMT2/TRDMT1 existed primarily as dimers via intermolecular disulfide bonds C79-C24, C292-C292, and C222-C24 in HEK293T cells. GSSG stress enhanced tRNA methylation level in the early stage of stress, whereas the DNMT2/TRDMT1 activity might be unfavorable along with this enzyme accumulation in the nucleus. Excitingly, GSH stress downregulated the DNMT2/TRDMT1 expression and promoted tRNA methylation in cells, probably through breaking intermolecular disulfide bonds in this enzyme. Thus, our findings demonstrated restricted tRNA methylation by disulfide bonds in DNMT2/TRDMT1, and will provide important implications for redox stress related-diseases.
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Affiliation(s)
- Huari Li
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China.
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yapeng Yang
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yunfei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Yong Chen
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Pingfang Xue
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Juan Chen
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Mian Qin
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Dandan Xu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Chao Cai
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Hongjing Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan 430070, Hubei, China
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3
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Lai H, Feng N, Zhai Q. Discovery of the major 15-30 nt mammalian small RNAs, their biogenesis and function. Nat Commun 2023; 14:5796. [PMID: 37723159 PMCID: PMC10507107 DOI: 10.1038/s41467-023-41554-6] [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: 02/07/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
Small RNAs (sRNAs) within 15-30 nt such as miRNA, tsRNA, srRNA with 3'-OH have been identified. However, whether these sRNAs are the major 15-30 nt sRNAs is still unknown. Here we show about 90% mammalian sRNAs within 15-30 nt end with 2',3'-cyclic phosphate (3'-cP). TANT-seq was developed to simultaneously profile sRNAs with 3'-cP (sRNA-cPs) and sRNA-OHs, and huge amount of sRNA-cPs were detected. Surprisingly, sRNA-cPs and sRNA-OHs usually have distinct sequences. The data from TANT-seq were validated by a novel method termed TE-qPCR, and Northern blot. Furthermore, we found that Angiogenin and RNase 4 contribute to the biogenesis of sRNA-cPs. Moreover, much more sRNA-cPs than sRNA-OHs bind to Ago2, and can regulate gene expression. Particularly, snR-2-cP regulates Bcl2 by targeting to its 3'UTR dependent on Ago2, and subsequently regulates apoptosis. In addition, sRNA-cPs can guide the cleavage of target RNAs in Ago2 complex as miRNAs without the requirement of 3'-cP. Our discovery greatly expands the repertoire of mammalian sRNAs, and provides strategies and powerful tools towards further investigation of sRNA-cPs.
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Affiliation(s)
- Hejin Lai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ning Feng
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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4
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Drewell RA, Cormier TC, Steenwyk JL, Denis JS, Tabima J, Dresch J, Larochelle D. The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing. NAR Genom Bioinform 2023; 5:lqad035. [PMID: 37081864 PMCID: PMC10111430 DOI: 10.1093/nargab/lqad035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/13/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing.
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Affiliation(s)
- Robert A Drewell
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Tayla C Cormier
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacob L Steenwyk
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James St Denis
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Javier F Tabima
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacqueline M Dresch
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Denis A Larochelle
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
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5
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Zimmermann R, Schwickert M, Meidner JL, Nidoieva Z, Helm M, Schirmeister T. An Optimized Microscale Thermophoresis Method for High-Throughput Screening of DNA Methyltransferase 2 Ligands. ACS Pharmacol Transl Sci 2022; 5:1079-1085. [PMID: 36407957 PMCID: PMC9667538 DOI: 10.1021/acsptsci.2c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 11/28/2022]
Abstract
Developing methyltransferase inhibitors is challenging, since most of the currently used assays are time-consuming and cost-intensive. Therefore, efficient, fast, and reliable methods for screenings and affinity determinations are of utmost importance. Starting from a literature-known fluorescent S-adenosylhomocysteine derivative, 5-FAM-triazolyl-adenosyl-Dab, developed for a fluorescence polarization assay to investigate the histone methyltransferase mixed-lineage leukemia 1, we herein describe the applicability of this compound as a fluorescent tracer for the investigation of DNA-methyltransferase 2 (DNMT2), a human RNA methyltransferase. Based on these findings, we established a microscale thermophoresis (MST) assay for DNMT2. This displacement assay can circumvent various problems inherent to this method. Furthermore, we optimized a screening method via MST which even indicates if the detected binding is competitive and gives the opportunity to estimate the potency of a ligand, both of which are not possible with a direct binding assay.
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Affiliation(s)
| | | | | | - Zarina Nidoieva
- Institute
of Pharmaceutical and Biomedical
Sciences, Johannes Gutenberg University
Mainz Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mark Helm
- Institute
of Pharmaceutical and Biomedical
Sciences, Johannes Gutenberg University
Mainz Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute
of Pharmaceutical and Biomedical
Sciences, Johannes Gutenberg University
Mainz Staudinger Weg 5, D-55128 Mainz, Germany
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6
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Chen M, Zhou L, Li S, Wei H, Chen J, Yang P, Peng H. Toxoplasma gondii DNA methyltransferases regulate parasitic energy metabolism. Acta Trop 2022; 229:106329. [PMID: 35122712 DOI: 10.1016/j.actatropica.2022.106329] [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: 10/19/2021] [Revised: 01/10/2022] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
The intracellular protozoan Toxoplasma gondii results in serious diseases such as encephalitis, and retinochoroiditis in immunocompromised patients. The interconversion between tachyzoites and bradyzoites under the host's immune pressure results in the interchange of acute infection and chronic infection. We previously reported two functional DNA methyltransferases (DNMT) in Toxoplasma gondii named TgDNMTa and TgDNMTb. In this research, proteomics analysis for T. gondii tachyzoites of ME49 WT, dnmta knockout (ME49-∆Tgdnmta), and dnmtb knockout (ME49-∆Tgdnmtb) strains, revealed 362 significantly regulated proteins for ME49-∆Tgdnmta, and 219 for ME49-∆Tgdnmtb, compared with the proteins of ME49 WT. TgDNMTa down regulated three glycolytic enzymes, one gluconeogenic enzyme and four pyruvate metabolic enzymes. Furthermore, TgDNMTb up regulated two proteins in the tricarboxylic acid (TCA) cycle. Glucose metabolic flux detection showed that TgDNMTa inhibited the glycolysis pathway, while TgDNMTb promoted the tricarboxylic acid (TCA) cycle so as to promote parasite's proliferation. These findings demonstrated that the functions of Toxoplasma gondii DNA methyltransferases extended beyond DNA methylation to the regulation of parasitic energy metabolism.
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Affiliation(s)
- Min Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Lijuan Zhou
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shengmin Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Hiaxia Wei
- Department of Pathogenic Biology, Guangzhou Medical University, Guangzhou 511436, China
| | - Jiating Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Pei Yang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Hongjuan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China.
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7
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Huang ZX, Li J, Xiong QP, Li H, Wang ED, Liu RJ. Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2. Nucleic Acids Res 2021; 49:13045-13061. [PMID: 34871455 PMCID: PMC8682788 DOI: 10.1093/nar/gkab1148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/05/2021] [Accepted: 11/03/2021] [Indexed: 12/05/2022] Open
Abstract
Dnmt2, a member of the DNA methyltransferase superfamily, catalyzes the formation of 5-methylcytosine at position 38 in the anticodon loop of tRNAs. Dnmt2 regulates many cellular biological processes, especially the production of tRNA-derived fragments and intergenerational transmission of paternal metabolic disorders to offspring. Moreover, Dnmt2 is closely related to human cancers. The tRNA substrates of mammalian Dnmt2s are mainly detected using bisulfite sequencing; however, we lack supporting biochemical data concerning their substrate specificity or recognition mechanism. Here, we deciphered the tRNA substrates of human DNMT2 (hDNMT2) as tRNAAsp(GUC), tRNAGly(GCC) and tRNAVal(AAC). Intriguingly, for tRNAAsp(GUC) and tRNAGly(GCC), G34 is the discriminator element; whereas for tRNAVal(AAC), the inosine modification at position 34 (I34), which is formed by the ADAT2/3 complex, is the prerequisite for hDNMT2 recognition. We showed that the C32U33(G/I)34N35 (C/U)36A37C38 motif in the anticodon loop, U11:A24 in the D stem, and the correct size of the variable loop are required for Dnmt2 recognition of substrate tRNAs. Furthermore, mammalian Dnmt2s possess a conserved tRNA recognition mechanism.
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MESH Headings
- 5-Methylcytosine/metabolism
- Adenosine Deaminase/genetics
- Adenosine Deaminase/metabolism
- Animals
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- DNA (Cytosine-5-)-Methyltransferases/chemistry
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- HEK293 Cells
- HeLa Cells
- Humans
- Inosine/metabolism
- Mice
- Models, Molecular
- NIH 3T3 Cells
- Nucleic Acid Conformation
- Protein Binding
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Gly/chemistry
- RNA, Transfer, Gly/genetics
- RNA, Transfer, Gly/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Substrate Specificity
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Affiliation(s)
- Zhi-Xuan Huang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
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8
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Li H, Zhu D, Wu J, Ma Y, Cai C, Chen Y, Qin M, Dai H. New substrates and determinants for tRNA recognition of RNA methyltransferase DNMT2/TRDMT1. RNA Biol 2021; 18:2531-2545. [PMID: 34110975 PMCID: PMC8632113 DOI: 10.1080/15476286.2021.1930756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/16/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Methylation is a common post-transcriptional modification of tRNAs, particularly in the anticodon loop region. The cytosine 38 (C38) in tRNAs, such as tRNAAsp-GUC, tRNAGly-GCC, tRNAVal-AAC, and tRNAGlu-CUC, can be methylated by human DNMT2/TRDMT1 and some homologs found in bacteria, plants, and animals. However, the substrate properties and recognition mechanism of DNMT2/TRDMT1 remain to be explored. Here, taking into consideration common features of the four known substrate tRNAs, we investigated methylation activities of DNMT2/TRDMT1 on the tRNAGly-GCC truncation and point mutants, and conformational changes of mutants. The results demonstrated that human DNMT2/TRDMT1 preferred substrate tRNAGly-GCC in vitro. L-shaped conformation of classical tRNA could be favourable for DNMT2/TRDMT1 activity. The complete sequence and structure of tRNA were dispensable for DNMT2/TRDMT1 activity, whereas T-arm was indispensable to this activity. G19, U20, and A21 in D-loop were identified as the important bases for DNMT2/TRDMT1 activity, while G53, C56, A58, and C61 in T-loop were found as the critical bases. The conserved CUXXCAC sequence in the anticodon loop was confirmed to be the most critical determinant, and it could stabilize C38-flipping to promote C38 methylation. Based on these tRNA properties, new substrates, tRNAVal-CAC and tRNAGln-CUG, were discovered in vitro. Moreover, a single nucleotide substitute, U32C, could convert non-substrate tRNAAla-AGC into a substrate for DNMT2/TRDMT1. Altogether, our findings imply that DNMT2/TRDMT1 relies on a delicate network involving both the primary sequence and tertiary structure of tRNA for substrate recognition.
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Affiliation(s)
- Huari Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jian Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yunfei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chao Cai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yong Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mian Qin
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hanchuan Dai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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9
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Gao Y, Fang J. RNA 5-methylcytosine modification and its emerging role as an epitranscriptomic mark. RNA Biol 2021; 18:117-127. [PMID: 34288807 DOI: 10.1080/15476286.2021.1950993] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
5-methylcytosine (m5C) is identified as an abundant and conserved modification in various RNAs, including tRNAs, mRNAs, rRNAs, and other non-coding RNAs. The application of high-throughput sequencing and mass spectrometry allowed for the detection of m5C at a single-nucleotide resolution and at a global abundance separately; this contributes to a better understanding of m5C modification and its biological functions. m5C modification plays critical roles in diverse aspects of RNA processing, including tRNA stability, rRNA assembly, and mRNA translation. Notably, altered m5C modifications and mutated RNA m5C methyltransferases are associated with diverse pathological processes, such as nervous system disorders and cancers. This review may provide new sights of molecular mechanism and functional importance of m5C modification.
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Affiliation(s)
- Yaqi Gao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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10
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Hoffmann A, Erber L, Betat H, Stadler PF, Mörl M, Fallmann J. Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum. Noncoding RNA 2021; 7:32. [PMID: 34071416 PMCID: PMC8163159 DOI: 10.3390/ncrna7020032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/23/2022] Open
Abstract
Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators of the translation process are affected by this transition. To this end, we used LOTTE-seq to sequence the tRNA pool of D. discoideum at different developmental time points and analyzed both tRNA composition and tRNA modification patterns. We developed a workflow for the specific detection of modifications from reverse transcriptase signatures in chemically untreated RNA-seq data at single-nucleotide resolution. It avoids the comparison of treated and untreated RNA-seq data using reverse transcription arrest patterns at nucleotides in the neighborhood of a putative modification site as internal control. We find that nucleotide modification sites in D. discoideum tRNAs largely conform to the modification patterns observed throughout the eukaroytes. However, there are also previously undescribed modification sites. We observe substantial dynamic changes of both expression levels and modification patterns of certain tRNA types during fruiting body development. Beyond the specific application to D. discoideum our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq.
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Affiliation(s)
- Anne Hoffmann
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany; (A.H.); (P.F.S.)
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at Leipzig University and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, D-04103 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany; (L.E.); (H.B.); (M.M.)
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany; (L.E.); (H.B.); (M.M.)
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany; (A.H.); (P.F.S.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, D-04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, 111321 Bogotá, D.C., Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany; (L.E.); (H.B.); (M.M.)
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany; (A.H.); (P.F.S.)
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11
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Zhu X, Wang X, Yan W, Yang H, Xiang Y, Lv F, Shi Y, Li HY, Lan L. Ubiquitination-mediated degradation of TRDMT1 regulates homologous recombination and therapeutic response. NAR Cancer 2021; 3:zcab010. [PMID: 33778494 PMCID: PMC7984809 DOI: 10.1093/narcan/zcab010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022] Open
Abstract
The RNA methyltransferase TRDMT1 has recently emerged as a key regulator of homologous recombination (HR) in the transcribed regions of the genome, but how it is regulated and its relevance in cancer remain unknown. Here, we identified that TRDMT1 is poly-ubiquitinated at K251 by the E3 ligase TRIM28, removing TRDMT1 from DNA damage sites and allowing completion of HR. Interestingly, K251 is adjacent to G155 in the 3D structure, and the G155V mutation leads to hyper ubiquitination of TRDMT1, reduced TRDMT1 levels and impaired HR. Accordingly, a TRDMT1 G155V mutation in an ovarian cancer super responder to platinum treatment. Cells expressing TRDMT1-G155V are sensitive to cisplatin in vitro and in vivo. In contrast, high expression of TRDMT1 in patients with ovarian cancer correlates with platinum resistance. A potent TRDMT1 inhibitor resensitizes TRDMT1-high tumor cells to cisplatin. These results suggest that TRDMT1 is a promising therapeutic target to sensitize ovarian tumors to platinum therapy.
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Affiliation(s)
- Xiaolan Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiangyu Wang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Haibo Yang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, 3501 fifth Ave., Pittsburgh, PA 15260, USA
| | - Fengping Lv
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, 3501 fifth Ave., Pittsburgh, PA 15260, USA
| | - Hong-yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
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12
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Gahlaut V, Samtani H, Khurana P. Genome-wide identification and expression profiling of cytosine-5 DNA methyltransferases during drought and heat stress in wheat (Triticum aestivum). Genomics 2020; 112:4796-4807. [PMID: 32890700 DOI: 10.1016/j.ygeno.2020.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023]
Abstract
DNA methylation is a potential epigenetic mechanism that regulates genome stability, development, and stress mitigation in plants. It is mediated by cytosine-5 DNA methyltransferases (C5-MTases). We identified 52 wheat C5-MTases; and based on domain structure and phylogenetics, these 52 C5-MTases were classified into four sub-families including MET, CMT, DRM and DNMT2; and were distributed on 18 chromosomes. Cis-acting regulatory elements analysis identified abiotic stress-responsive, phytohormone-responsive, development-related and light-related elements in the promoters of TaC5-MTases. We also examined the transcript abundance of TaC5-MTases in different tissues, developmental stages and under abiotic stresses. Notably, most of the TaC5-MTases (TaCMT2, TaCMT3b, TaCMT3c, TaMET1, TaDRM10, TaDNMT2) showed differential regulation of their transcript abundance during drought and heat stress. Overall, the above results provide significant insights into the expression and the probable functions of TaC5-MTases and will also expedite future research programs to explore the mechanisms of epigenetic regulation in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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13
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Erber L, Hoffmann A, Fallmann J, Hagedorn M, Hammann C, Stadler PF, Betat H, Prohaska S, Mörl M. Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum. Int J Mol Sci 2020; 21:ijms21155210. [PMID: 32717856 PMCID: PMC7432833 DOI: 10.3390/ijms21155210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023] Open
Abstract
Dictyostelium discoideum, the model organism for the evolutionary supergroup of Amoebozoa, is a social amoeba that, upon starvation, undergoes transition from a unicellular to a multicellular organism. In its genome, we identified two genes encoding for tRNA nucleotidyltransferases. Such pairs of tRNA nucleotidyltransferases usually represent collaborating partial activities catalyzing CC- and A-addition to the tRNA 3'-end, respectively. In D. discoideum, however, both enzymes exhibit identical activities, representing bona-fide CCA-adding enzymes. Detailed characterization of the corresponding activities revealed that both enzymes seem to be essential and are regulated inversely during different developmental stages of D. discoideum. Intriguingly, this is the first description of two functionally equivalent CCA-adding enzymes using the same set of tRNAs and showing a similar distribution within the cell. This situation seems to be a common feature in Dictyostelia, as other members of this phylum carry similar pairs of tRNA nucleotidyltransferase genes in their genome.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
| | - Anne Hoffmann
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
| | - Jörg Fallmann
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
| | - Monica Hagedorn
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany; (M.H.); (C.H.)
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany; (M.H.); (C.H.)
| | - Peter F. Stadler
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, 04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Carrera 45 No. 26-85, Colombia
- Santa Fe Institute for Complex Systems, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Department of Theoretical Chemistry of the University of Vienna, A-1090 Vienna, Austria
| | - Heike Betat
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
| | - Sonja Prohaska
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
- Computational EvoDevo Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
- Correspondence: ; Tel.: +49-341-9736-911; Fax: +49-341-9736-919
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14
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Furlan M, Tanaka I, Leonardi T, de Pretis S, Pelizzola M. Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts. Front Genet 2020; 11:394. [PMID: 32425981 PMCID: PMC7212349 DOI: 10.3389/fgene.2020.00394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/30/2020] [Indexed: 01/24/2023] Open
Abstract
It has been known for a few decades that transcripts can be marked by dozens of different modifications. Yet, we are just at the beginning of charting these marks and understanding their functional impact. High-quality methods were developed for the profiling of some of these marks, and approaches to finely study their impact on specific phases of the RNA life-cycle are available, including RNA metabolic labeling. Thanks to these improvements, the most abundant marks, including N6-methyladenosine, are emerging as important determinants of the fate of marked RNAs. However, we still lack approaches to directly study how the set of marks for a given RNA molecule shape its fate. In this perspective, we first review current leading approaches in the field. Then, we propose an experimental and computational setup, based on direct RNA sequencing and mathematical modeling, to decipher the functional consequences of RNA modifications on the fate of individual RNA molecules and isoforms.
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Affiliation(s)
- Mattia Furlan
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
- Department of Physics, National Institute of Nuclear Physics, University of Turin, Turin, Italy
| | - Iris Tanaka
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tommaso Leonardi
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Stefano de Pretis
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
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15
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Singh D, Yadav R, Kaushik S, Wadhwa N, Kapoor S, Kapoor M. Transcriptome Analysis of ppdnmt2 and Identification of Superoxide Dismutase as a Novel Interactor of DNMT2 in the Moss Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2020; 11:1185. [PMID: 32849734 PMCID: PMC7419982 DOI: 10.3389/fpls.2020.01185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/21/2020] [Indexed: 05/07/2023]
Abstract
DNMT2 is a DNA/tRNA cytosine methyltransferase that is highly conserved in structure and function in eukaryotes. In plants however, limited information is available on the function of this methyltransferase. We have previously reported that in the moss Physcomitrella patens, DNMT2 plays a crucial role in stress recovery and tRNAAsp transcription/stability under salt stress. To further investigate the role of PpDNMT2 at genome level, in this study we have performed RNA sequencing of ppdnmt2. Transcriptome analysis reveals a number of genes and pathways to function differentially and suggests a close link between PpDNMT2 function and osmotic and ionic stress tolerance. We propose PpDNMT2 to play a pivotal role in regulating salt tolerance by affecting molecular networks involved in stress perception and signal transduction that underlie maintenance of ion homeostasis in cells. We also examined interactome of PpDNMT2 using affinity purification (AP) coupled to mass spectrometry (AP-MS). Quantitative proteomic analysis reveals several chloroplast proteins involved in light reactions and carbon assimilation and proteins involved in stress response and some not implicated in stress to co-immunoprecipitate with PpDNMT2. Comparison between transcriptome and interactome datasets has revealed novel association between PpDNMT2 activity and the antioxidant enzyme Superoxide dismutase (SOD), protein turnover mediated by the Ubiquitin-proteasome system and epigenetic gene regulation. PpDNMT2 possibly exists in complex with CuZn-SODs in vivo and the two proteins also directly interact in the yeast nucleus as observed by yeast two-hybrid assay. Taken together, the work presented in this study sheds light on diverse roles of PpDNMT2 in maintaining molecular and physiological homeostasis in P. patens. This is a first report describing transcriptome and interactome of DNMT2 in any land plant.
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Affiliation(s)
- Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Radha Yadav
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Shubham Kaushik
- Vproteomics, Valerian Chem Private Limited Green Park Mains, New Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
- *Correspondence: Meenu Kapoor,
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16
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Bohnsack KE, Höbartner C, Bohnsack MT. Eukaryotic 5-methylcytosine (m⁵C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease. Genes (Basel) 2019; 10:genes10020102. [PMID: 30704115 PMCID: PMC6409601 DOI: 10.3390/genes10020102] [Citation(s) in RCA: 274] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/04/2023] Open
Abstract
5-methylcytosine (m⁵C) is an abundant RNA modification that's presence is reported in a wide variety of RNA species, including cytoplasmic and mitochondrial ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as messenger RNAs (mRNAs), enhancer RNAs (eRNAs) and a number of non-coding RNAs. In eukaryotes, C5 methylation of RNA cytosines is catalyzed by enzymes of the NOL1/NOP2/SUN domain (NSUN) family, as well as the DNA methyltransferase homologue DNMT2. In recent years, substrate RNAs and modification target nucleotides for each of these methyltransferases have been identified, and structural and biochemical analyses have provided the first insights into how each of these enzymes achieves target specificity. Functional characterizations of these proteins and the modifications they install have revealed important roles in diverse aspects of both mitochondrial and nuclear gene expression. Importantly, this knowledge has enabled a better understanding of the molecular basis of a number of diseases caused by mutations in the genes encoding m⁵C methyltransferases or changes in the expression level of these enzymes.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Justus-von-Liebig-Weg 11, 37077 Germany.
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17
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García-Vílchez R, Sevilla A, Blanco S. Post-transcriptional regulation by cytosine-5 methylation of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:240-252. [PMID: 30593929 DOI: 10.1016/j.bbagrm.2018.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/02/2023]
Abstract
The recent advent of high-throughput sequencing technologies coupled with RNA modifications detection methods has allowed the detection of RNA modifications at single nucleotide resolution giving a more comprehensive landscape of post-transcriptional gene regulation pathways. In this review, we focus on the occurrence of 5-methylcytosine (m5C) in the transcriptome. We summarise the main findings of the molecular role in post-transcriptional regulation that governs m5C deposition in RNAs. Functionally, m5C deposition can regulate several cellular and physiological processes including development, differentiation and survival to stress stimuli. Despite many aspects concerning m5C deposition in RNA, such as position or sequence context and the fact that many readers and erasers still remain elusive, the overall recent findings indicate that RNA cytosine methylation is a powerful mechanism to post-transcriptionally regulate physiological processes. In addition, mutations in RNA cytosine-5 methyltransferases are associated to pathological processes ranging from neurological syndromes to cancer.
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Affiliation(s)
| | - Ana Sevilla
- Physiology, Cellular Biology and Immunology Department - Biology Faculty. University of Barcelona, Avda. Diagonal 643, 08028 Barcelona. Spain
| | - Sandra Blanco
- CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain..
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18
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Romano G, Veneziano D, Nigita G, Nana-Sinkam SP. RNA Methylation in ncRNA: Classes, Detection, and Molecular Associations. Front Genet 2018; 9:243. [PMID: 30050561 PMCID: PMC6052889 DOI: 10.3389/fgene.2018.00243] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/20/2018] [Indexed: 11/25/2022] Open
Abstract
Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification, as more than 150 distinct modification types have been reported. Since RNA modifications were first described over 50 years ago, our understanding of their functional relevance in cellular control mechanisms and phenotypes has truly progressed only in the last 15 years due to advancements in detection and experimental techniques. Specifically, the phenomenon of RNA methylation in the context of ncRNA has emerged as a novel process in the arena of epitranscriptomics. Methylated ncRNA molecules may indeed contribute to a potentially vast functional panorama, from regulation of post-transcriptional gene expression to adaptive cellular responses. Recent discoveries have uncovered novel dynamic mechanisms and new layers of complexity, paving the way to a greater understanding of the role of such phenomena within the broader molecular cellular context of human disease.
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Affiliation(s)
- Giulia Romano
- Internal Medicine "Division of Pulmonary and Critical Care Medicine", Virginia Commonwealth University Health System, Richmond, VA, United States
| | - Dario Veneziano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
| | - Serge P Nana-Sinkam
- Internal Medicine "Division of Pulmonary and Critical Care Medicine", Virginia Commonwealth University Health System, Richmond, VA, United States
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19
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Haag S, Sloan KE, Höbartner C, Bohnsack MT. In Vitro Assays for RNA Methyltransferase Activity. Methods Mol Biol 2018; 1562:259-268. [PMID: 28349466 DOI: 10.1007/978-1-4939-6807-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
RNA methyltransferases (MTases) are responsible for co- and posttranscriptional methylation of nucleotides in a wide variety of RNA substrates. Examination of the target specificity, catalytic activity, and function of these enzymes requires in vitro methylation assays. Here, we provide a detailed protocol for the methylation of in vitro transcripts, synthetic RNAs, and total cellular RNA using recombinant RNA methyltransferases and S-adenosylmethionine (SAM) as a methyl group donor. We describe how this method can be coupled to fluorographic detection of RNA methylation if 3H-labeled SAM is used, and discuss alternative chromatography-based methods for the detection of methylated nucleotides, focusing on reversed-phase high-performance liquid chromatography (RP-HPLC). In both cases, mutagenesis of the methyltransferase or the RNA substrate can be employed to elucidate the catalytic mechanisms and target specificity of the enzymes. Together these approaches provide valuable insight into the action of RNA methyltransferases on the molecular level and serve as a basis for further functional characterization of RNA methyltransferases in vivo.
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Affiliation(s)
- Sara Haag
- Centre for Biochemistry and Molecular Cell Biology, Institute for Molecular Biology, Georg-August-University, Humboldtallee 23, 37073, Göttingen, Germany
| | - Katherine E Sloan
- Centre for Biochemistry and Molecular Cell Biology, Institute for Molecular Biology, Georg-August-University, Humboldtallee 23, 37073, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077, Göttingen, Germany
| | - Markus T Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Institute for Molecular Biology, Georg-August-University, Humboldtallee 23, 37073, Göttingen, Germany. .,Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073, Göttingen, Germany.
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20
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Bartelt SM, Chervyachkova E, Steinkühler J, Ricken J, Wieneke R, Tampé R, Dimova R, Wegner SV. Dynamic blue light-switchable protein patterns on giant unilamellar vesicles. Chem Commun (Camb) 2018; 54:948-951. [DOI: 10.1039/c7cc08758f] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The photoswitchable iLID/Nano interaction allows for specific, non-invasive, reversible and dynamic protein photopatterning on GUVs with high spatiotemporal control.
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Affiliation(s)
- S. M. Bartelt
- Max Planck Institute for Polymer Research
- Mainz
- Germany
| | | | - J. Steinkühler
- Department of Theory and Biosystems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
| | - J. Ricken
- Max Planck Institute for Polymer Research
- Mainz
- Germany
| | - R. Wieneke
- Institut für Biochemie, Biozentrum
- Cluster of Excellence Frankfurt
- Goethe-Universität Frankfurt
- Frankfurt
- Germany
| | - R. Tampé
- Institut für Biochemie, Biozentrum
- Cluster of Excellence Frankfurt
- Goethe-Universität Frankfurt
- Frankfurt
- Germany
| | - R. Dimova
- Department of Theory and Biosystems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
| | - S. V. Wegner
- Max Planck Institute for Polymer Research
- Mainz
- Germany
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21
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Lewinska A, Adamczyk-Grochala J, Kwasniewicz E, Wnuk M. Downregulation of methyltransferase Dnmt2 results in condition-dependent telomere shortening and senescence or apoptosis in mouse fibroblasts. J Cell Physiol 2017; 232:3714-3726. [PMID: 28177119 DOI: 10.1002/jcp.25848] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 01/05/2023]
Abstract
Dnmt2 is a highly conserved methyltransferase of uncertain biological function(s). As Dnmt2 was considered as a driver of fruit fly longevity and a modulator of stress response, we decided to evaluate the role of Dnmt2 during stress-induced premature senescence in NIH3T3 mouse fibroblasts. Stable knockdown of Dnmt2 resulted in hydrogen peroxide-mediated sensitivity and apoptosis, whereas in the control conditions, senescence was induced. Cellular senescence was accompanied by elevated levels of p53 and p21, decreased telomere length and telomerase activity, increased production of reactive oxygen species and protein carbonylation, and DNA damage. Dnmt2 silencing also promoted global DNA and RNA hypermethylation, and upregulation of methyltransferases, namely Dnmt1, Dnmt3a, and Dnmt3b. Taken together, we show for the first time that Dnmt2 may promote lifespan in the control conditions and survival during stress conditions in mouse fibroblasts.
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Affiliation(s)
- Anna Lewinska
- Laboratory of Cell Biology, University of Rzeszow, Kolbuszowa, Poland
| | | | - Ewa Kwasniewicz
- Laboratory of Cell Biology, University of Rzeszow, Kolbuszowa, Poland
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Kolbuszowa, Poland
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22
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Quantitative Systems Biology to decipher design principles of a dynamic cell cycle network: the "Maximum Allowable mammalian Trade-Off-Weight" (MAmTOW). NPJ Syst Biol Appl 2017; 3:26. [PMID: 28944079 PMCID: PMC5605530 DOI: 10.1038/s41540-017-0028-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022] Open
Abstract
Network complexity is required to lend cellular processes flexibility to respond timely to a variety of dynamic signals, while simultaneously warranting robustness to protect cellular integrity against perturbations. The cell cycle serves as a paradigm for such processes; it maintains its frequency and temporal structure (although these may differ among cell types) under the former, but accelerates under the latter. Cell cycle molecules act together in time and in different cellular compartments to execute cell type-specific programs. Strikingly, the timing at which molecular switches occur is controlled by abundance and stoichiometry of multiple proteins within complexes. However, traditional methods that investigate one effector at a time are insufficient to understand how modulation of protein complex dynamics at cell cycle transitions shapes responsiveness, yet preserving robustness. To overcome this shortcoming, we propose a multidisciplinary approach to gain a systems-level understanding of quantitative cell cycle dynamics in mammalian cells from a new perspective. By suggesting advanced experimental technologies and dedicated modeling approaches, we present innovative strategies (i) to measure absolute protein concentration in vivo, and (ii) to determine how protein dosage, e.g., altered protein abundance, and spatial (de)regulation may affect timing and robustness of phase transitions. We describe a method that we name “Maximum Allowable mammalian Trade–Off–Weight” (MAmTOW), which may be realized to determine the upper limit of gene copy numbers in mammalian cells. These aspects, not covered by current systems biology approaches, are essential requirements to generate precise computational models and identify (sub)network-centered nodes underlying a plethora of pathological conditions.
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Govindaraju G, Jabeena CA, Sethumadhavan DV, Rajaram N, Rajavelu A. DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1047-1057. [PMID: 28847733 DOI: 10.1016/j.bbagrm.2017.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 11/28/2022]
Abstract
In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite.
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Affiliation(s)
- Gayathri Govindaraju
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India
| | - C A Jabeena
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India
| | | | - Nivethika Rajaram
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India
| | - Arumugam Rajavelu
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India.
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Kaiser S, Jurkowski TP, Kellner S, Schneider D, Jeltsch A, Helm M. The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA. RNA Biol 2016; 14:1241-1251. [PMID: 27819523 PMCID: PMC5699543 DOI: 10.1080/15476286.2016.1236170] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The amino acid sequence of Dnmt2 is very similar to the catalytic domains of bacterial and eukaryotic DNA-(cytosine 5)-methyltransferases, but it efficiently catalyzes tRNA methylation, while its DNA methyltransferase activity is the subject of controversial reports with rates varying between zero and very weak. By using composite nucleic acid molecules as substrates, we surprisingly found that DNA fragments, when presented as covalent DNA-RNA hybrids in the structural context of a tRNA, can be more efficiently methylated than the corresponding natural tRNA substrate. Furthermore, by stepwise development of tRNAAsp, we showed that this natural Dnmt2 substrate could be engineered to employ RNAs that act like guide RNAs in vitro. The 5’-half of tRNAAsp was able to efficiently guide methylation toward a single stranded tRNA fragment as would result from tRNA cleavage by tRNA specific nucleases. In a more artificial setting, a composite system of guide RNAs could ultimately be engineered to enable the enzyme to perform cytidine methylation on single stranded DNA in vitro.
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Affiliation(s)
- Steffen Kaiser
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Tomasz P Jurkowski
- b Institute of Biochemistry, Faculty of Chemistry, University Stuttgart , Stuttgart , Germany
| | - Stefanie Kellner
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Dirk Schneider
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Albert Jeltsch
- b Institute of Biochemistry, Faculty of Chemistry, University Stuttgart , Stuttgart , Germany
| | - Mark Helm
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
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26
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Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, Rodnina MV, Höbartner C, Bohnsack MT. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. EMBO J 2016; 35:2104-2119. [PMID: 27497299 PMCID: PMC5048346 DOI: 10.15252/embj.201694885] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial gene expression uses a non‐universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt‐)tRNAMet mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt‐tRNAMet to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m5C34 of mt‐tRNAMet to generate an f5C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilisation of m5C34 mt‐tRNAMet in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt‐tRNAMet function. Together, our data reveal how modifications in mt‐tRNAMet are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNAMet to recognise the different codons encoding methionine.
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Affiliation(s)
- Sara Haag
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ahmed S Warda
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jens Kretschmer
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Charlotte Blessing
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Benedikt Hübner
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Jan Seikowski
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sven Dennerlein
- Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany
| | - Peter Rehling
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Institute for Cellular Biochemistry, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, University Medical Center Göttingen Georg-August-University, Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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Jeltsch A, Ehrenhofer-Murray A, Jurkowski TP, Lyko F, Reuter G, Ankri S, Nellen W, Schaefer M, Helm M. Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation. RNA Biol 2016; 14:1108-1123. [PMID: 27232191 PMCID: PMC5699548 DOI: 10.1080/15476286.2016.1191737] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about a decade ago. Between the presumed involvement in DNA modification-related epigenetics, and the recent foray into the RNA modification field, significant progress has characterized Dnmt2-related research. Here, we review this progress in its diverse facets including molecular evolution, structural biology, biochemistry, chemical biology, cell biology and epigenetics.
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Affiliation(s)
- Albert Jeltsch
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | | | - Tomasz P Jurkowski
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | - Frank Lyko
- c Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center , Heidelberg , Germany
| | - Gunter Reuter
- d Institute of Biology, Developmental Genetics, Martin Luther University Halle , Halle , Germany
| | - Serge Ankri
- e Department of Molecular Microbiology , The Bruce Rappaport Faculty of Medicine , Technion , Haifa , Israel
| | - Wolfgang Nellen
- f Abteilung für Genetik, Universität Kassel , Kassel , Germany
| | - Matthias Schaefer
- g Medical University of Vienna, Center for Anatomy & Cell Biology , Vienna , Austria
| | - Mark Helm
- h Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Mainz , Germany
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28
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Arya D, Kapoor S, Kapoor M. Physcomitrella patens DNA methyltransferase 2is required for recovery from salt and osmotic stress. FEBS J 2016; 283:556-70. [DOI: 10.1111/febs.13611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/06/2015] [Accepted: 11/25/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Deepshikha Arya
- University School of Biotechnology; Guru Gobind Singh Indraprastha University; New Delhi India
| | - Sanjay Kapoor
- Department of Plant Molecular Biology; Interdisciplinary Centre for Plant Genomics; University of Delhi; India
| | - Meenu Kapoor
- University School of Biotechnology; Guru Gobind Singh Indraprastha University; New Delhi India
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29
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Abstract
tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, methylation reactions are by far the most abundant. The tRNA methyltransferases comprise a diverse enzyme superfamily, including members of multiple structural classes that appear to have arisen independently during evolution. Even among closely related family members, examples of unusual substrate specificity and chemistry have been observed. Here we review recent advances in tRNA methyltransferase mechanism and function with a particular emphasis on discoveries of alternative substrate specificities and chemistry associated with some methyltransferases. Although the molecular function for a specific tRNA methylation may not always be clear, mutations in tRNA methyltransferases have been increasingly associated with human disease. The impact of tRNA methylation on human biology is also discussed.
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Affiliation(s)
- William E Swinehart
- a Center for RNA Biology and Department of Chemistry and Biochemistry ; Ohio State University ; Columbus , OH USA
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Gaston KW, Limbach PA. The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry. RNA Biol 2015; 11:1568-85. [PMID: 25616408 PMCID: PMC4615682 DOI: 10.4161/15476286.2014.992280] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.
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Affiliation(s)
- Kirk W Gaston
- a Rieveschl Laboratories for Mass Spectrometry; Department of Chemistry ; University of Cincinnati ; Cincinnati , OH USA
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31
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Müller M, Hartmann M, Schuster I, Bender S, Thüring KL, Helm M, Katze JR, Nellen W, Lyko F, Ehrenhofer-Murray AE. Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Nucleic Acids Res 2015; 43:10952-62. [PMID: 26424849 PMCID: PMC4678861 DOI: 10.1093/nar/gkv980] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dnmt2 enzymes are cytosine-5 methyltransferases that methylate C38 of several tRNAs. We report here that the activities of two Dnmt2 homologs, Pmt1 from Schizosaccharomyces pombe and DnmA from Dictyostelium discoideum, are strongly stimulated by prior queuosine (Q) modification of the substrate tRNA. In vivo tRNA methylation levels were stimulated by growth of cells in queuine-containing medium; in vitro Pmt1 activity was enhanced on Q-containing RNA; and queuine-stimulated in vivo methylation was abrogated by the absence of the enzyme that inserts queuine into tRNA, eukaryotic tRNA-guanine transglycosylase. Global analysis of tRNA methylation in S. pombe showed a striking selectivity of Pmt1 for tRNA(Asp) methylation, which distinguishes Pmt1 from other Dnmt2 homologs. The present analysis also revealed a novel Pmt1- and Q-independent tRNA methylation site in S. pombe, C34 of tRNA(Pro). Notably, queuine is a micronutrient that is scavenged by higher eukaryotes from the diet and gut microflora. This work therefore reveals an unanticipated route by which the environment can modulate tRNA modification in an organism.
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Affiliation(s)
- Martin Müller
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mark Hartmann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Kathrin L Thüring
- Institut für Pharmakologie und Biochemie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Mark Helm
- Institut für Pharmakologie und Biochemie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Jon R Katze
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Wolfgang Nellen
- Abteilung für Genetik, Universität Kassel, 34132 Kassel, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
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Haag S, Warda AS, Kretschmer J, Günnigmann MA, Höbartner C, Bohnsack MT. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA (NEW YORK, N.Y.) 2015; 21:1532-43. [PMID: 26160102 PMCID: PMC4536315 DOI: 10.1261/rna.051524.115] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/01/2015] [Indexed: 05/04/2023]
Abstract
Many cellular RNAs require modification of specific residues for their biogenesis, structure, and function. 5-methylcytosine (m(5)C) is a common chemical modification in DNA and RNA but in contrast to the DNA modifying enzymes, only little is known about the methyltransferases that establish m(5)C modifications in RNA. The putative RNA methyltransferase NSUN6 belongs to the family of Nol1/Nop2/SUN domain (NSUN) proteins, but so far its cellular function has remained unknown. To reveal the target spectrum of human NSUN6, we applied UV crosslinking and analysis of cDNA (CRAC) as well as chemical crosslinking with 5-azacytidine. We found that human NSUN6 is associated with tRNAs and acts as a tRNA methyltransferase. Furthermore, we uncovered tRNA(Cys) and tRNA(Thr) as RNA substrates of NSUN6 and identified the cytosine C72 at the 3' end of the tRNA acceptor stem as the target nucleoside. Interestingly, target recognition in vitro depends on the presence of the 3'-CCA tail. Together with the finding that NSUN6 localizes to the cytoplasm and largely colocalizes with marker proteins for the Golgi apparatus and pericentriolar matrix, our data suggest that NSUN6 modifies tRNAs in a late step in their biogenesis.
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Affiliation(s)
- Sara Haag
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Ahmed S Warda
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Jens Kretschmer
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Manuel A Günnigmann
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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Shanmugam R, Fierer J, Kaiser S, Helm M, Jurkowski TP, Jeltsch A. Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences. Cell Discov 2015; 1:15010. [PMID: 27462411 PMCID: PMC4860778 DOI: 10.1038/celldisc.2015.10] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/26/2015] [Indexed: 01/09/2023] Open
Abstract
The Dnmt2 RNA methyltransferase catalyses the methylation of C38 in the anticodon loop of tRNA-Asp, but the molecular role of this methylation is unknown. Here, we report that mouse aspartyl-tRNA synthetase shows a four to fivefold preference for C38-methylated tRNA-Asp. Consistently, a 30% reduced charging level of tRNA-Asp was observed in Dnmt2 knockout (KO) murine embryonic fibroblast cells. Gene expression analysis with fluorescent reporter proteins fused to an N-terminal poly-Asp sequence showed that protein synthesis of poly-Asp-tagged reporter proteins was reduced in Dnmt2 KO cells as well. The same effect was observed with endogenous proteins containing poly-Asp sequences, indicating that Dnmt2-mediated C38 methylation of tRNA-Asp regulates the translation of proteins containing poly-Asp sequences. Gene ontology searches for proteins containing poly-Asp sequences in the human proteome showed that a significant number of these proteins have roles in transcriptional regulation and gene expression. Hence, the Dnmt2-mediated methylation of tRNA-Asp exhibits a post-transcriptional regulatory role by controlling the synthesis of a group of target proteins containing poly-Asp sequences.
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Affiliation(s)
- Raghuvaran Shanmugam
- Institute of Biochemistry, Stuttgart University, Faculty of Chemistry , Stuttgart, Germany
| | - Jacob Fierer
- MoLife Program, School of Engineering and Science, Jacobs University Bremen , Bremen, Germany
| | - Steffen Kaiser
- Institute of Pharmacy and Biochemistry, Faculty of Chemistry, Pharmaceutical Sciences and Geoscience, Johannes Gutenberg-Universität Mainz , Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Faculty of Chemistry, Pharmaceutical Sciences and Geoscience, Johannes Gutenberg-Universität Mainz , Mainz, Germany
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, Faculty of Chemistry , Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Faculty of Chemistry , Stuttgart, Germany
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Egg-specific expression of protein with DNA methyltransferase activity in the biocarcinogenic liver fluke Clonorchis sinensis. Parasitology 2015; 142:1228-38. [PMID: 26036304 DOI: 10.1017/s0031182015000566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Despite recent reports regarding the biology of cytosine methylation in Schistosoma mansoni, the impact of the regulatory machinery remains unclear in diverse platyhelminthes. This ambiguity is reinforced by discoveries of DNA methyltransferase 2 (DNMT2)-only organisms and the substrate specificity of DNMT2 preferential to RNA molecules. Here, we characterized a novel DNA methyltransferase, named CsDNMT2, in a liver fluke Clonorchis sinensis. The protein exhibited structural properties conserved in other members of the DNMT2 family. The native and recombinant CsDNMT2 exhibited considerable enzymatic activity on DNA. The spatiotemporal expression of CsDNMT2 mirrored that of 5-methylcytosine (5 mC), both of which were elevated in the C. sinensis eggs. However, CsDNMT2 and 5 mC were marginally detected in other histological regions of C. sinensis adults including ovaries and seminal receptacle. The methylation site seemed not related to genomic loci occupied by progenies of an active long-terminal-repeat retrotransposon. Taken together, our data strongly suggest that C. sinensis has preserved the functional DNA methylation machinery and that DNMT2 acts as a genuine alternative to DNMT1/DNMT3 to methylate DNA in the DNMT2-only organism. The epigenetic regulation would target functional genes primarily involved in the formation and/or maturation of eggs, rather than retrotransposons.
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Abstract
Cells have developed molecular machineries, which can chemically modify DNA and RNA nucleosides. One particular and chemically simple modification, (cytosine-5) methylation (m(5)C), has been detected both in RNA and DNA suggesting universal use of m(5)C for the function of these nucleotide polymers. m(5)C can be reproducibly mapped to abundant noncoding RNAs (transfer RNA, tRNA and ribosomal RNA, rRNA), and recently, also nonabundant RNAs (including mRNAs) have been reported to carry this modification. Quantification of m(5)C content in total RNA preparations indicates that a limited number of RNAs carry this modification and suggests specific functions for (cytosine-5) RNA methylation. What exactly is the biological function of m(5)C in RNA? Before attempting to address this question, m(5)C needs to be mapped specifically and reproducibly, preferably on a transcriptome-wide scale. To facilitate the detection of m(5)C in its sequence context, RNA bisulfite sequencing (RNA-BisSeq) has been developed. This method relies on the efficient chemical deamination of nonmethylated cytosine, which can be read out as single nucleotide polymorphism (nonmethylated cytosine as thymine vs. methylated cytosine as cytosine), when differentially comparing cDNA libraries to reference sequences after DNA sequencing. Here, the basic protocol of RNA-BisSeq, its current applications and limitations are described.
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Affiliation(s)
- Matthias Schaefer
- Vienna Biocenter, Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Universität Wien, Vienna, Austria.
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Elhardt W, Shanmugam R, Jurkowski TP, Jeltsch A. Somatic cancer mutations in the DNMT2 tRNA methyltransferase alter its catalytic properties. Biochimie 2015; 112:66-72. [PMID: 25747896 DOI: 10.1016/j.biochi.2015.02.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/24/2015] [Indexed: 12/22/2022]
Abstract
Methylation of tRNA is an important post-transcriptional modification and aberrations in tRNA modification has been implicated in cancer. The DNMT2 protein methylates C38 of tRNA-Asp and it has a role in cellular physiology and stress response and its expression levels are altered in cancer tissues. Here we studied whether DNMT2 somatic mutations found in cancer tissues affect the activity of the enzyme. We have generated 13 DNMT2 variants and purified the corresponding proteins. All proteins were properly folded as determined by circular dichroism spectroscopy. We tested their RNA methylation activity using in vitro generated tRNA-Asp. One of the mutations (E63K) caused a twofold increase in activity, while two of them led to a strong (over fourfold) decrease in activity (G155S and L257V). Two additional mutant proteins were almost inactive (R371H and G155V). The strong effect of some of the somatic cancer mutations on DNMT2 activity suggests that these mutations have a functional role in tumorigenesis.
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Affiliation(s)
- Winfried Elhardt
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | | | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
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37
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Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1440-53. [DOI: 10.1016/j.bbagrm.2014.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/22/2023]
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Boesler B, Meier D, Förstner KU, Friedrich M, Hammann C, Sharma CM, Nellen W. Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. J Biol Chem 2014; 289:35124-38. [PMID: 25352599 DOI: 10.1074/jbc.m114.612663] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA- strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA- strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA-/agnB- double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA- strains was observed.
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Affiliation(s)
- Benjamin Boesler
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Doreen Meier
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Konrad U Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Michael Friedrich
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Laboratory, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University, Campus Ring 1, DE-28759 Bremen, Germany
| | - Cynthia M Sharma
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Wolfgang Nellen
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany,
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Miceli M, Bontempo P, Nebbioso A, Altucci L. Natural compounds in epigenetics: a current view. Food Chem Toxicol 2014; 73:71-83. [PMID: 25139119 DOI: 10.1016/j.fct.2014.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 01/03/2023]
Abstract
The successful treatment of many human diseases, including cancer, has come to be considered a major challenge, as patient response to therapy is difficult to predict. Recently, considerable efforts are being focused on the development of new tools to meet the growing demand for personalized medicine. With few exceptions, synthetic compounds have been unable to meet initial expectations for their clinical use. The last twenty years have been characterized by the failure of several drugs in advanced clinical development, possibly due to the insufficient understanding of molecular pathways underlying their mechanism of action. Although the biodiversity of compounds found in nature has been poorly explored until now, the field of naturally occurring drugs is rapidly expanding. Here, we review the current knowledge on the use of natural compounds with particular emphasis on those that display a chromatin remodeling effect coupled with anticancer action.
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Affiliation(s)
- Marco Miceli
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati-Traverso, IGB, Via P. Castellino 111, 80131 Napoli, Italy
| | - Paola Bontempo
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Angela Nebbioso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati-Traverso, IGB, Via P. Castellino 111, 80131 Napoli, Italy.
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Shanmugam R, Aklujkar M, Schäfer M, Reinhardt R, Nickel O, Reuter G, Lovley DR, Ehrenhofer-Murray A, Nellen W, Ankri S, Helm M, Jurkowski TP, Jeltsch A. The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. Nucleic Acids Res 2014; 42:6487-96. [PMID: 24711368 PMCID: PMC4041430 DOI: 10.1093/nar/gku256] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.
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Affiliation(s)
| | - Muktak Aklujkar
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Matthias Schäfer
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Olaf Nickel
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, 06120 Halle, Germany
| | - Gunter Reuter
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, 06120 Halle, Germany
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
| | | | - Wolfgang Nellen
- Department of Genetics, University of Kassel, 34132 Kassel, Germany
| | - Serge Ankri
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
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Abstract
Post-transcriptional cleavage of RNA molecules to generate smaller fragments is a widespread mechanism that enlarges the structural and functional complexity of cellular RNomes. Substrates for such RNA fragmentations are coding as well as non-protein-coding RNAs. In particular, fragments derived from both precursor and mature tRNAs represent one of the rapidly growing classes of post-transcriptional RNA pieces. Importantly, these tRNA fragments possess distinct expression patterns, abundance, cellular localizations, or biological roles compared with their parental tRNA molecules. Here we review recent reports on tRNA cleavage and attempt to categorize tRNA pieces according to their origin and cellular function. The biological scope of tRNA-derived fragments ranges from translation control, over RNA silencing, to regulating apoptosis, and thus clearly enlarges the functional repertoire of ncRNA biology.
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Affiliation(s)
- Jennifer Gebetsberger
- Department of Chemistry and Biochemistry; University of Bern; Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences; University of Bern; Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry; University of Bern; Bern, Switzerland; Division of Genomics and RNomics; Medical University Innsbruck; Innsbruck, Austria
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