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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [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] [Indexed: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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2
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Hayashi T, Daitoku H, Uetake T, Kako K, Fukamizu A. Histidine Nτ-methylation identified as a new posttranslational modification in histone H2A at His-82 and H3 at His-39. J Biol Chem 2023; 299:105131. [PMID: 37543365 PMCID: PMC10485160 DOI: 10.1016/j.jbc.2023.105131] [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: 04/06/2023] [Revised: 07/24/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023] Open
Abstract
Histone posttranslational modifications play critical roles in a variety of eukaryotic cellular processes. In particular, methylation at lysine and arginine residues is an epigenetic mark that determines the chromatin state. In addition, histone "histidine" methylation was initially reported over 50 years ago; however, further studies in this area were not conducted, leaving a gap in our understanding. Here, we aimed to investigate the occurrence of histidine methylation in histone proteins using highly sensitive mass spectrometry. We found that acid hydrolysates of whole histone fraction from calf thymus contained Nτ-methylhistidine, but not Nπ-methylhistidine. Both core and linker histones carried a Nτ-methylhistidine modification, and methylation levels were relatively high in histone H3. Furthermore, through MALDI-TOF MS, we identified two histidine methylation sites at His-82 in the structured globular domain of histone H2A and His-39 in the N-terminal tail of histones H3. Importantly, these histidine methylation signals were also detected in histones purified from a human cell line HEK293T. Moreover, we revealed the overall methylation status of histone H3, suggesting that methylation is enriched primarily at lysine residues and to a lesser extent at arginine and histidine residues. Thus, our findings established histidine Nτ-methylation as a new histone modification, which may serve as a chemical flag that mediates the epigenetic mark of adjacent residues of the N-terminal tail and the conformational properties of the globular domain.
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Affiliation(s)
- Takahiro Hayashi
- Doctoral Program in Life and Agricultural Sciences, Degree Programs in Life and Earth Sciences, Graduate School of Sciences and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Toru Uetake
- Doctoral Program in Life and Agricultural Sciences, Degree Programs in Life and Earth Sciences, Graduate School of Sciences and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Koichiro Kako
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan; International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, Japan.
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3
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Kasai F, Kako K, Maruhashi S, Uetake T, Yao Y, Daitoku H, Fukamizu A. γ-enolase (ENO2) is methylated at the Nτ position of His-190 among enolase isozymes. J Biochem 2023; 174:279-289. [PMID: 37279646 DOI: 10.1093/jb/mvad042] [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: 02/23/2023] [Revised: 05/16/2023] [Accepted: 06/03/2023] [Indexed: 06/08/2023] Open
Abstract
Protein methylation is mainly observed in lysine, arginine and histidine residues. Histidine methylation occurs at one of two different nitrogen atoms of the imidazole ring, producing Nτ-methylhistidine and Nπ-methylhistidine, and it has recently attracted attention with the identification of SETD3, METTL18 and METTL9 as catalytic enzymes in mammals. Although accumulating evidence had suggested the presence of more than 100 proteins containing methylated histidine residues in cells, much less information has been known regarding histidine-methylated proteins than lysine- and arginine-methylated ones, because no method has been developed to identify substrates for histidine methylation. Here, we established a method to screen novel target proteins for histidine methylation, using biochemical protein fractionation combined with the quantification of methylhistidine by LC-MS/MS. Interestingly, the differential distribution pattern of Nτ-methylated proteins was found between the brain and skeletal muscle, and identified γ-enolase where the His-190 at the Nτ position is methylated in mouse brain. Finally, in silico structural prediction and biochemical analysis showed that the His-190 in γ-enolase is involved in the intermolecular homodimeric formation and enzymatic activity. In the present study, we provide a new methodology to find histidine-methylated proteins in vivo and suggest an insight into the importance of histidine methylation.
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Key Words
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Nτ-methylhistidine.Abbreviations: ADMA, asymmetric dimethylarginine; DML, dimethyllysine; HEK293T, human embryonic kidney 293T; HIC, hydrophobic interaction chromatography; LC-MS/MS, liquid chromatography-tandem mass spectrometry; MALDI-TOF/MS, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; MMA, monomethylarginine; MRM, multiple reaction monitoring; N-PLA, N-propyl-L-arginine; SAM, S-adenosylmethionine; SDMA, symmetric dimethylarginine; TML, trimethyllysine
- Mus musculus
- enolase
- histidine methylation
- γ-enolase
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Affiliation(s)
- Fumiya Kasai
- Doctoral Program in Life and Agricultural Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Koichiro Kako
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Syunsuke Maruhashi
- Degree Program in Agro-Bioresources Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Toru Uetake
- Doctoral Program in Life and Agricultural Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yuan Yao
- Ph.D. Program in Human Biology, School of Integrative Global Majors (SIGMA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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Barchi JJ, Strain CN. The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation. Front Mol Biosci 2023; 10:1117850. [PMID: 36845552 PMCID: PMC9950641 DOI: 10.3389/fmolb.2023.1117850] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
A variety of glycan structures cover the surface of all cells and are involved in myriad biological processes, including but not limited to, cell adhesion and communication, protein quality control, signal transduction and metabolism, while also being intimately involved in innate and adaptive immune functions. Immune surveillance and responses to foreign carbohydrate antigens, such as capsular polysaccharides on bacteria and surface protein glycosylation of viruses, are the basis of microbial clearance, and most antimicrobial vaccines target these structures. In addition, aberrant glycans on tumors called Tumor-Associated Carbohydrate Antigens (TACAs) elicit immune responses to cancer, and TACAs have been used in the design of many antitumor vaccine constructs. A majority of mammalian TACAs are derived from what are referred to as mucin-type O-linked glycans on cell-surface proteins and are linked to the protein backbone through the hydroxyl group of either serine or threonine residues. A small group of structural studies that have compared mono- and oligosaccharides attached to each of these residues have shown that there are distinct differences in conformational preferences assumed by glycans attached to either "unmethylated" serine or ß-methylated threonine. This suggests that the linkage point of antigenic glycans will affect their presentation to the immune system as well as to various carbohydrate binding molecules (e.g., lectins). This short review, followed by our hypothesis, will examine this possibility and extend the concept to the presentation of glycans on surfaces and in assay systems where recognition of glycans by proteins and other binding partners can be defined by different attachment points that allow for a range of conformational presentations.
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Affiliation(s)
| | - Caitlin N. Strain
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute at Frederick, Frederick, MD, United States
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Chen X, Johnson RM, Li B. A Permissive Amide N-Methyltransferase for Dithiolopyrrolones. ACS Catal 2023; 13:1899-1905. [PMID: 38106463 PMCID: PMC10720983 DOI: 10.1021/acscatal.2c05439] [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] [Indexed: 01/19/2023]
Abstract
Amide N-methylation is important for the activity and permeability of bioactive compounds but can be challenging to perform selectively. The broad-spectrum antimicrobial natural products thiolutin and holomycin differ only by an N-methyl group at the endocyclic amide of thiolutin, but only thiolutin exhibits antifungal activity. The enzyme responsible for amide N--methylation in thiolutin biosynthesis has remained elusive. Here, we identified and characterized the amide N-methyltransferase DtpM that is encoded >400 kb outside of the thiolutin gene cluster. DtpM catalyzes efficient conversion of holomycin to thiolutin, exhibits broad substrate scope toward dithiolopyrrolones, and has high thermal stability. In addition, sequence similarity network analysis suggests DtpM is more closely related to phenol O-methyltransferases than some amide methyltransferases. This study expands the limited examples of amide N-methyltransferases and may facilitate chemoenzymatic synthesis of diverse dithiolopyrrolone compounds as potential therapeutics.
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Affiliation(s)
- Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rachel M Johnson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, and Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Ying Y, Li X, Chen Y. Hypomethylation of the opioid receptor delta 1 gene combined with high opioid receptor delta 1 protein levels indicates increased risk of gout. J Clin Lab Anal 2022; 36:e24634. [PMID: 35908776 PMCID: PMC9459328 DOI: 10.1002/jcla.24634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
Background The purpose of this study was to identify biomarkers for the diagnosis of gout in Chinese Han males using methylation microarray profiling. Methods We screened for differentially methylated genes (DMGs) in gout using a methylation microarray and analyzed the functions of the DMGs using gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We verified gene methylation levels by pyrosequencing and protein levels by enzyme‐linked immunosorbent assays (ELISAs). Statistical analyses were performed using SPSS. Two‐sided p values <0.05 were deemed to be statistically significant for all analyses. Results We identified 20,426 significant differential methylation sites (5719 high‐methylation sites and 14,707 low‐methylation sites). Bioinformatics analysis showed that the DMGs were mainly involved in 43 biological functions, 13 cellular components, 18 molecular functions, and 35 KEGG pathways. We selected opioid receptor delta 1 (OPRD1) for verification of methylation levels between 50 gout patients and 50 controls. The methylation levels of OPRD1 (Chr1:29,139,121) were significantly lower in the gout group (p < 0.05), while OPRD1 protein levels were significantly higher in the gout group (p < 0.05). In addition, the AUC of the combination of OPRD1 (Chr1:29,139,121) methylation and OPRD1 protein levels was 0.796 (0.710, 0.883) with a high sensitivity of 82% and a specificity of 68% (p < 0.001). Conclusions The combination of OPRD1 (Chr1:29,139,121) hypomethylation and high levels of OPRD1 protein is a potential biomarker for gout diagnosis.
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Affiliation(s)
- Ying Ying
- Department of Rheumatology, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), Ningbo, Zhejiang, China
| | - Xiaoke Li
- Medical School, Ningbo University, Ningbo, Zhejiang, China
| | - Yong Chen
- Department of Rheumatology, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), Ningbo, Zhejiang, China
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7
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Daitoku H, Someya M, Kako K, Hayashi T, Tajima T, Haruki H, Sekiguchi N, Uetake T, Akimoto Y, Fukamizu A. siRNA screening identifies METTL9 as a histidine Nπ-methyltransferase that targets the proinflammatory protein S100A9. J Biol Chem 2021; 297:101230. [PMID: 34562450 PMCID: PMC8571522 DOI: 10.1016/j.jbc.2021.101230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
Protein methylation is one of the most common post-translational modifications observed in basic amino acid residues, including lysine, arginine, and histidine. Histidine methylation occurs on the distal or proximal nitrogen atom of its imidazole ring, producing two isomers: Nτ-methylhistidine or Nπ-methylhistidine. However, the biological significance of protein histidine methylation remains largely unclear owing in part to the very limited knowledge about its contributing enzymes. Here, we identified mammalian seven-β-strand methyltransferase METTL9 as a histidine Nπ-methyltransferase by siRNA screening coupled with methylhistidine analysis using LC–tandem MS. We demonstrated that METTL9 catalyzes Nπ-methylhistidine formation in the proinflammatory protein S100A9, but not that of myosin light chain kinase MYLK2, in vivo and in vitro. METTL9 does not affect the heterodimer formation of S100A9 and S100A8, although Nπ-methylation of S100A9 at His-107 overlaps with a zinc-binding site, attenuating its affinity for zinc. Given that S100A9 exerts an antimicrobial activity, probably by chelation of zinc essential for the growth of bacteria and fungi, METTL9-mediated S100A9 methylation might be involved in the innate immune response to bacterial and fungal infection. Thus, our findings suggest a functional consequence for protein histidine Nπ-methylation and may add a new layer of complexity to the regulatory mechanisms of post-translational methylation.
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Affiliation(s)
- Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Momoka Someya
- Master's Program in Agro-Bioresources Science and Technology, Degree Programs in Life and Earth Sciences, Graduate School of Sciences and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Koichiro Kako
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takahiro Hayashi
- Doctoral Program in Life and Agricultural Sciences, Degree Programs in Life and Earth Sciences, Graduate School of Sciences and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tatsuya Tajima
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hikari Haruki
- Master's Program in Agro-Bioresources Science and Technology, Degree Programs in Life and Earth Sciences, Graduate School of Sciences and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Naoki Sekiguchi
- College of Agro-Biological Resource Sciences, School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Toru Uetake
- Master's Program in Agro-Bioresources Science and Technology, Degree Programs in Life and Earth Sciences, Graduate School of Sciences and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuto Akimoto
- College of Agro-Biological Resource Sciences, School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan; The World Premier International Research Center Initiative (WPI), International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, Japan.
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8
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Chan K, Li X. Current Epigenetic Insights in Kidney Development. Genes (Basel) 2021; 12:genes12081281. [PMID: 34440455 PMCID: PMC8391601 DOI: 10.3390/genes12081281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/07/2021] [Accepted: 08/19/2021] [Indexed: 12/31/2022] Open
Abstract
The kidney is among the best characterized developing tissues, with the genes and signaling pathways that regulate embryonic and adult kidney patterning and development having been extensively identified. It is now widely understood that DNA methylation and histone modification patterns are imprinted during embryonic development and must be maintained in adult cells for appropriate gene transcription and phenotypic stability. A compelling question then is how these epigenetic mechanisms play a role in kidney development. In this review, we describe the major genes and pathways that have been linked to epigenetic mechanisms in kidney development. We also discuss recent applications of single-cell RNA sequencing (scRNA-seq) techniques in the study of kidney development. Additionally, we summarize the techniques of single-cell epigenomics, which can potentially be used to characterize epigenomes at single-cell resolution in embryonic and adult kidneys. The combination of scRNA-seq and single-cell epigenomics will help facilitate the further understanding of early cell lineage specification at the level of epigenetic modifications in embryonic and adult kidney development, which may also be used to investigate epigenetic mechanisms in kidney diseases.
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Affiliation(s)
- Katrina Chan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA;
| | - Xiaogang Li
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-266-0110
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9
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Shima H, Igarashi K. N 1-methyladenosine (m1A) RNA modification: the key to ribosome control. J Biochem 2021; 167:535-539. [PMID: 32129871 DOI: 10.1093/jb/mvaa026] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 11/14/2022] Open
Abstract
RNA displays diverse functions in living cells. The presence of various chemical modifications of RNA mediated by enzymes is one of the factors that impart such functional diversity to RNA. Among more than 100 types of RNA modification, N1-methyladenosine (m1A) is found mainly in tRNA and rRNA of many living organisms and is known to be deeply implicated in the topology or function of the two classes of RNA. In this commentary article, we would like to deal with the functional significance of m1A in RNA, and also to describe one methyltransferase installing m1A in a large subunit rRNA, whose orthologue in Caenorhabditis elegans was discovered recently and was reported in this journal.
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Affiliation(s)
- Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine.,Regulatory Epigenome, Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, Miyagi 980-8575, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine.,Regulatory Epigenome, Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, Miyagi 980-8575, Japan
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10
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Ma M, Chen X, Yin Y, Fan R, Li B, Zhan Y, Zeng F. DNA Methylation Silences Exogenous Gene Expression in Transgenic Birch Progeny. FRONTIERS IN PLANT SCIENCE 2020; 11:523748. [PMID: 33414793 PMCID: PMC7783445 DOI: 10.3389/fpls.2020.523748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/28/2020] [Indexed: 05/04/2023]
Abstract
The genetic stability of exogenous genes in the progeny of transgenic trees is extremely important in forest breeding; however, it remains largely unclear. We selected transgenic birch (Betula platyphylla) and its hybrid F1 progeny to investigate the expression stability and silencing mechanism of exogenous genes. We found that the exogenous genes of transgenic birch could be transmitted to their offspring through sexual reproduction. The exogenous genes were segregated during genetic transmission. The hybrid progeny of transgenic birch WT1×TP22 (184) and WT1×TP23 (212) showed higher Bgt expression and greater insect resistance than their parents. However, the hybrid progeny of transgenic birch TP23×TP49 (196) showed much lower Bgt expression, which was only 13.5% of the expression in its parents. To elucidate the mechanism underlying the variation in gene expression between the parents and progeny, we analyzed the methylation rates of Bgt in its promoter and coding regions. The hybrid progeny with normally expressed exogenous genes showed much lower methylation rates (0-29%) than the hybrid progeny with silenced exogenous genes (32.35-45.95%). These results suggest that transgene silencing in the progeny is mainly due to DNA methylation at cytosine residues. We further demonstrated that methylation in the promoter region, rather than in the coding region, leads to gene silencing. We also investigated the relative expression levels of three methyltransferase genes: BpCMT, BpDRM, and BpMET. The transgenic birch line 196 with a silenced Gus gene showed, respectively, 2.54, 9.92, and 4.54 times higher expression levels of BpCMT, BpDRM, and BpMET than its parents. These trends are consistent with and corroborate the high methylation levels of exogenous genes in the transgenic birch line 196. Therefore, our study suggests that DNA methylation in the promoter region leads to silencing of exogenous genes in transgenic progeny of birch.
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Affiliation(s)
- Minghao Ma
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xiaohui Chen
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yibo Yin
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ruixin Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Bo Li
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yaguang Zhan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Fansuo Zeng
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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11
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Kornfuehrer T, Romanowski S, de Crécy-Lagard V, Hanson AD, Eustáquio AS. An Enzyme Containing the Conserved Domain of Unknown Function DUF62 Acts as a Stereoselective (R s ,S c )-S-Adenosylmethionine Hydrolase. Chembiochem 2020; 21:3495-3499. [PMID: 32776704 DOI: 10.1002/cbic.202000349] [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: 06/02/2020] [Revised: 08/07/2020] [Indexed: 11/09/2022]
Abstract
Homochirality is a signature of biological systems. The essential and ubiquitous cofactor S-adenosyl-l-methionine (SAM) is synthesized in cells from adenosine triphosphate and l-methionine to yield exclusively the (S,S)-SAM diastereomer. (S,S)-SAM plays a crucial role as the primary methyl donor in transmethylation reactions important to the development and homeostasis of all organisms from bacteria to humans. However, (S,S)-SAM slowly racemizes at the sulfonium center to yield the inactive (R,S)-SAM, which can inhibit methyltransferases. Control of SAM homochirality has been shown to involve homocysteine S-methyltransferases in plants, insects, worms, yeast, and in ∼18 % of bacteria. Herein, we show that a recombinant protein containing a domain of unknown function (DUF62) from the actinomycete bacterium Salinispora tropica functions as a stereoselective (R,S)-SAM hydrolase (adenosine-forming). DUF62 proteins are encoded in the genomes of 21 % of bacteria and 42 % of archaea and potentially represent a novel mechanism to remediate SAM damage.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Pharmaceutical Sciences and, Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Sean Romanowski
- Department of Pharmaceutical Sciences and, Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science and, Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Alessandra S Eustáquio
- Department of Pharmaceutical Sciences and, Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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White JT, Cato T, Deramchi N, Gabunilas J, Roy KR, Wang C, Chanfreau GF, Clarke SG. Protein Methylation and Translation: Role of Lysine Modification on the Function of Yeast Elongation Factor 1A. Biochemistry 2019; 58:4997-5010. [PMID: 31738538 DOI: 10.1021/acs.biochem.9b00818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1-7 and Rkm 1-5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 and Efm4-7) appear to be specific to elongation factor 1A (EF1A), the protein responsible for bringing aminoacyl-tRNAs to the ribosome. In S. cerevisiae, the functional implications of lysine methylation in translation are mostly unknown. In this work, we assessed the physiological impact of disrupting EF1A methylation in a strain where four of the most conserved methylated lysine sites are mutated to arginine residues and in strains lacking either four or five of the Efm lysine methyltransferases specific to EF1A. We found that loss of EF1A methylation was not lethal but resulted in reduced growth rates, particularly under caffeine and rapamycin stress conditions, suggesting EF1A interacts with the TORC1 pathway, as well as altered sensitivities to ribosomal inhibitors. We also detected reduced cellular levels of the EF1A protein, which surprisingly was not reflected in its stability in vivo. We present evidence that these Efm methyltransferases appear to be largely devoted to the modification of EF1A, finding no evidence of the methylation of other substrates in the yeast cell. This work starts to illuminate why one protein can need five different methyltransferases for its functions and highlights the resilience of yeast to alterations in their posttranslational modifications.
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Affiliation(s)
- Jonelle T White
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Tieranee Cato
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Neil Deramchi
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Kevin R Roy
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Charles Wang
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
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