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Wang YC, Chang CP, Lai YC, Chan CH, Ou SC, Wang SH, Li C. The conservation and diversity of the exons encoding the glycine and arginine rich domain of the fibrillarin gene in vertebrates, with special focus on reptiles and birds. Gene 2023; 866:147345. [PMID: 36893875 DOI: 10.1016/j.gene.2023.147345] [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: 09/05/2022] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
The nucleolar rRNA 2'-O-methyltransferase fibrillarin (FBL) contains a highly conserved methyltransferase domain at the C-terminus and a diverse glycine arginine-rich (GAR) domain at the N-terminus in eukaryotes. We found that a nine-exon configuration of fbl and exon 2-3 encoded GAR domain are conserved and specific in vertebrates. All internal exons except exon 2 and 3 are of the same lengths in different vertebrate lineages. The lengths of exon 2 and 3 vary in different vertebrate species but the ones with longer exon 2 usually have shorter exon 3 complementarily, limiting lengths of the GAR domain within a certain range. In tetrapods except for reptiles, exon 2 appears to be longer than exon 3. We specifically analyzed different lineages of reptiles for their GAR sequences and exon lengths. The lengths of exon 2 in reptiles are around 80-130-nt shorter and the lengths of exon 3 in reptiles are around 50-90 nt longer than those in other tetrapods, all in the GAR-coding regions. An FSPR sequence is present at the beginning of the GAR domain encoded by exon 2 in all vertebrates, and a specific FXSP/G element (X can be K, R, Q, N, and H) exist in the middle of GAR with phenylalanine as the 3rd exon 3-encoded amino acid residue starting from jawfish. Snakes, turtles, and songbirds contain shorter exon 2 compared with lizards, indicating continuous deletions in exon 2 and insertions/duplications in exon 3 in these lineages. Specifically, we confirmed the presence the fbl gene in chicken and validated the RNA expression. Our analyses of the GAR-encoding exons of fbl in vertebrates and reptiles should provide the basis for further evolutionary analyses of more GAR domain encoding proteins.
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Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chien-Ping Chang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Chuan Lai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chi-Ho Chan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan; Department of Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Shan-Chia Ou
- Department of Veterinary Medicine, Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Sue-Hong Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chuan Li
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
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2
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Cura V, Cavarelli J. Structure, Activity and Function of the PRMT2 Protein Arginine Methyltransferase. Life (Basel) 2021; 11:1263. [PMID: 34833139 PMCID: PMC8623767 DOI: 10.3390/life11111263] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
PRMT2 belongs to the protein arginine methyltransferase (PRMT) family, which catalyzes the arginine methylation of target proteins. As a type I enzyme, PRMT2 produces asymmetric dimethyl arginine and has been shown to have weak methyltransferase activity on histone substrates in vitro, suggesting that its authentic substrates have not yet been found. PRMT2 contains the canonical PRMT methylation core and a unique Src homology 3 domain. Studies have demonstrated its clear implication in many different cellular processes. PRMT2 acts as a coactivator of several nuclear hormone receptors and is known to interact with a multitude of splicing-related proteins. Furthermore, PRMT2 is aberrantly expressed in several cancer types, including breast cancer and glioblastoma. These reports highlight the crucial role played by PRMT2 and the need for a better characterization of its activity and cellular functions.
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Affiliation(s)
- Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
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3
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Palli SR. Epigenetic regulation of post-embryonic development. CURRENT OPINION IN INSECT SCIENCE 2021; 43:63-69. [PMID: 33068783 PMCID: PMC8044252 DOI: 10.1016/j.cois.2020.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 05/02/2023]
Abstract
Modifications to DNA and core histones influence chromatin organization and expression of the genome. DNA methylation plays a significant role in the regulation of multiple biological processes that regulate behavior and caste differentiation in social insects. Histone modifications play significant roles in the regulation of development and reproduction in other insects. Genes coding for acetyltransferases, deacetylases, methyltransferases, and demethylases that modify core histones have been identified in genomes of multiple insects. Studies on the function and mechanisms of action of some of these enzymes uncovered their contribution to post-embryonic development. The results from studies on epigenetic modifiers could help in the identification of inhibitors of epigenetic modifiers that could be developed to control pests and disease vectors.
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Affiliation(s)
- Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, S225 Ag. Science N, Lexington, KY 40546, United States.
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Fulton MD, Brown T, Zheng YG. Mechanisms and Inhibitors of Histone Arginine Methylation. CHEM REC 2018; 18:1792-1807. [PMID: 30230223 PMCID: PMC6348102 DOI: 10.1002/tcr.201800082] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022]
Abstract
Histone methylation plays an important regulatory role in chromatin restructuring and RNA transcription. Arginine methylation that is enzymatically catalyzed by the family of protein arginine methyltransferases (PRMTs) can either activate or repress gene expression depending on cellular contexts. Given the strong correlation of PRMTs with pathophysiology, great interest is seen in understanding molecular mechanisms of PRMTs in diseases and in developing potent PRMT inhibitors. Herein, we reviewed key research advances in the study of biochemical mechanisms of PRMT catalysis and their relevance to cell biology. We highlighted how a random binary, ordered ternary kinetic model for PRMT1 catalysis reconciles the literature reports and endorses a distributive mechanism that the enzyme active site utilizes for multiple turnovers of arginine methylation. We discussed the impacts of histone arginine methylation and its biochemical interplays with other key epigenetic marks. Challenges in developing small-molecule PRMT inhibitors were also discussed.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA 30602
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA 30602
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA 30602
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5
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Hadjikyriacou A, Clarke SG. Caenorhabditis elegans PRMT-7 and PRMT-9 Are Evolutionarily Conserved Protein Arginine Methyltransferases with Distinct Substrate Specificities. Biochemistry 2017; 56:2612-2626. [PMID: 28441492 DOI: 10.1021/acs.biochem.7b00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Caenorhabditis elegans protein arginine methyltransferases PRMT-7 and PRMT-9 are two evolutionarily conserved enzymes, with distinct orthologs in plants, invertebrates, and vertebrates. Biochemical characterization of these two enzymes reveals that they share much in common with their mammalian orthologs. C. elegans PRMT-7 produces only monomethylarginine (MMA) and preferentially methylates R-X-R motifs in a broad collection of substrates, including human histone peptides and RG-rich peptides. In addition, the activity of the PRMT-7 enzyme is dependent on temperature, the presence of metal ions, and the reducing agent dithiothreitol. C. elegans PRMT-7 has a substrate specificity and a substrate preference different from those of mammalian PRMT7, and the available X-ray crystal structures of the PRMT7 orthologs show differences in active site architecture. C. elegans PRMT-9, on the other hand, produces symmetric dimethylarginine and MMA on SFTB-2, the conserved C. elegans ortholog of human RNA splicing factor SF3B2, indicating a possible role in the regulation of nematode splicing. In contrast to PRMT-7, C. elegans PRMT-9 appears to be biochemically indistinguishable from its human ortholog.
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Affiliation(s)
- Andrea Hadjikyriacou
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
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Kafková L, Debler EW, Fisk JC, Jain K, Clarke SG, Read LK. The Major Protein Arginine Methyltransferase in Trypanosoma brucei Functions as an Enzyme-Prozyme Complex. J Biol Chem 2016; 292:2089-2100. [PMID: 27998975 DOI: 10.1074/jbc.m116.757112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/14/2016] [Indexed: 11/06/2022] Open
Abstract
Prozymes are catalytically inactive enzyme paralogs that dramatically stimulate the function of weakly active enzymes through complex formation. The two prozymes described to date reside in the polyamine biosynthesis pathway of the human parasite Trypanosoma brucei, an early branching eukaryote that lacks transcriptional regulation and regulates its proteome through posttranscriptional and posttranslational means. Arginine methylation is a common posttranslational modification in eukaryotes catalyzed by protein arginine methyltransferases (PRMTs) that are typically thought to function as homodimers. We demonstrate that a major T. brucei PRMT, TbPRMT1, functions as a heterotetrameric enzyme-prozyme pair. The inactive PRMT paralog, TbPRMT1PRO, is essential for catalytic activity of the TbPRMT1ENZ subunit. Mutational analysis definitively demonstrates that TbPRMT1ENZ is the cofactor-binding subunit and carries all catalytic activity of the complex. Our results are the first demonstration of an obligate heteromeric PRMT, and they suggest that enzyme-prozyme organization is expanded in trypanosomes as a posttranslational means of enzyme regulation.
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Affiliation(s)
- Lucie Kafková
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Erik W Debler
- the Laboratory of Cell Biology, The Rockefeller University, New York, New York 10065, and
| | - John C Fisk
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Kanishk Jain
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Laurie K Read
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214,
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Cura V, Marechal N, Troffer-Charlier N, Strub JM, van Haren MJ, Martin NI, Cianférani S, Bonnefond L, Cavarelli J. Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors. FEBS J 2016; 284:77-96. [PMID: 27879050 DOI: 10.1111/febs.13953] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/27/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022]
Abstract
PRMT2 is the less-characterized member of the protein arginine methyltransferase family in terms of structure, activity, and cellular functions. PRMT2 is a modular protein containing a catalytic Ado-Met-binding domain and unique Src homology 3 domain that binds proteins with proline-rich motifs. PRMT2 is involved in a variety of cellular processes and has diverse roles in transcriptional regulation through different mechanisms depending on its binding partners. PRMT2 has been demonstrated to have weak methyltransferase activity on a histone H4 substrate, but its optimal substrates have not yet been identified. To obtain insights into the function and activity of PRMT2, we solve several crystal structures of PRMT2 from two homologs (zebrafish and mouse) in complex with either the methylation product S-adenosyl-L-homocysteine or other compounds including the first synthetic PRMT2 inhibitor (Cp1) studied so far. We reveal that the N-terminal-containing SH3 module is disordered in the full-length crystal structures, and highlights idiosyncratic features of the PRMT2 active site. We identify a new nonhistone protein substrate belonging to the serine-/arginine-rich protein family which interacts with PRMT2 and we characterize six methylation sites by mass spectrometry. To better understand structural basis for Cp1 binding, we also solve the structure of the complex PRMT4:Cp1. We compare the inhibitor-protein interactions occurring in the PRMT2 and PRMT4 complex crystal structures and show that this compound inhibits efficiently PRMT2. These results are a first step toward a better understanding of PRMT2 substrate recognition and may accelerate the development of structure-based drug design of PRMT2 inhibitors. DATABASE All coordinates and structure factors have been deposited in the Protein Data Bank: zPRMT21-408 -SFG = 5g02; zPRMT273-408 -SAH = 5fub; mPRMT21-445 -SAH = 5ful; mPRMT21-445 -Cp1 = 5fwa, mCARM1130-487 -Cp1 = 5k8v.
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Affiliation(s)
- Vincent Cura
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U596, Université de Strasbourg, Illkirch, France
| | - Nils Marechal
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U596, Université de Strasbourg, Illkirch, France
| | - Nathalie Troffer-Charlier
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U596, Université de Strasbourg, Illkirch, France
| | - Jean-Marc Strub
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, UMR7178, Université de Strasbourg, France
| | - Matthijs J van Haren
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, UMR7178, Université de Strasbourg, France
| | - Luc Bonnefond
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U596, Université de Strasbourg, Illkirch, France
| | - Jean Cavarelli
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U596, Université de Strasbourg, Illkirch, France
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8
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Yang WF, Yu ZG, Anh V. Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation. Mol Phylogenet Evol 2015; 96:102-111. [PMID: 26724405 DOI: 10.1016/j.ympev.2015.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/18/2023]
Abstract
UNLABELLED Traditional methods for sequence comparison and phylogeny reconstruction rely on pair wise and multiple sequence alignments. But alignment could not be directly applied to whole genome/proteome comparison and phylogenomic studies due to their high computational complexity. Hence alignment-free methods became popular in recent years. Here we propose a fast alignment-free method for whole genome/proteome comparison and phylogeny reconstruction using higher order Markov model and chaos game representation. In the present method, we use the transition matrices of higher order Markov models to characterize amino acid or DNA sequences for their comparison. The order of the Markov model is uniquely identified by maximizing the average Shannon entropy of conditional probability distributions. Using one-dimensional chaos game representation and linked list, this method can reduce large memory and time consumption which is due to the large-scale conditional probability distributions. To illustrate the effectiveness of our method, we employ it for fast phylogeny reconstruction based on genome/proteome sequences of two species data sets used in previous published papers. Our results demonstrate that the present method is useful and efficient. AVAILABILITY AND IMPLEMENTATION The source codes for our algorithm to get the distance matrix and genome/proteome sequences can be downloaded from ftp://121.199.20.25/. The software Phylip and EvolView we used to construct phylogenetic trees can be referred from their websites.
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Affiliation(s)
- Wei-Feng Yang
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China; Department of Mathematics and Physics, Hunan Institute of Engineering, Hunan 411104, PR China.
| | - Zu-Guo Yu
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China; School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Vo Anh
- School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
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Hadjikyriacou A, Yang Y, Espejo A, Bedford MT, Clarke SG. Unique Features of Human Protein Arginine Methyltransferase 9 (PRMT9) and Its Substrate RNA Splicing Factor SF3B2. J Biol Chem 2015; 290:16723-43. [PMID: 25979344 DOI: 10.1074/jbc.m115.659433] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 12/29/2022] Open
Abstract
Human protein arginine methyltransferase (PRMT) 9 symmetrically dimethylates arginine residues on splicing factor SF3B2 (SAP145) and has been functionally linked to the regulation of alternative splicing of pre-mRNA. Site-directed mutagenesis studies on this enzyme and its substrate had revealed essential unique residues in the double E loop and the importance of the C-terminal duplicated methyltransferase domain. In contrast to what had been observed with other PRMTs and their physiological substrates, a peptide containing the methylatable Arg-508 of SF3B2 was not recognized by PRMT9 in vitro. Although amino acid substitutions of residues surrounding Arg-508 had no great effect on PRMT9 recognition of SF3B2, moving the arginine residue within this sequence abolished methylation. PRMT9 and PRMT5 are the only known mammalian enzymes capable of forming symmetric dimethylarginine (SDMA) residues as type II PRMTs. We demonstrate here that the specificity of these enzymes for their substrates is distinct and not redundant. The loss of PRMT5 activity in mouse embryo fibroblasts results in almost complete loss of SDMA, suggesting that PRMT5 is the primary SDMA-forming enzyme in these cells. PRMT9, with its duplicated methyltransferase domain and conserved sequence in the double E loop, appears to have a unique structure and specificity among PRMTs for methylating SF3B2 and potentially other polypeptides.
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Affiliation(s)
- Andrea Hadjikyriacou
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los, Angeles, California 90095 and
| | - Yanzhong Yang
- the Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Alexsandra Espejo
- the Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Mark T Bedford
- the Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los, Angeles, California 90095 and
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