1
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Yeh MC, Hsu NH, Chu HY, Yang CH, Hsu PH, Chou CC, Shie JT, Lee WM, Ho MC, Lo KY. Dual protection by Bcp1 and Rkm1 ensures incorporation of uL14 into pre-60S ribosomal subunits. J Cell Biol 2024; 223:e202306117. [PMID: 39007857 PMCID: PMC11248248 DOI: 10.1083/jcb.202306117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/13/2024] [Accepted: 04/19/2024] [Indexed: 07/16/2024] Open
Abstract
Eukaryotic ribosomal proteins contain extended regions essential for translation coordination. Dedicated chaperones stabilize the associated ribosomal proteins. We identified Bcp1 as the chaperone of uL14 in Saccharomyces cerevisiae. Rkm1, the lysine methyltransferase of uL14, forms a ternary complex with Bcp1 and uL14 to protect uL14. Rkm1 is transported with uL14 by importins to the nucleus, and Bcp1 disassembles Rkm1 and importin from uL14 simultaneously in a RanGTP-independent manner. Molecular docking, guided by crosslinking mass spectrometry and validated by a low-resolution cryo-EM map, reveals the correlation between Bcp1, Rkm1, and uL14, demonstrating the protection model. In addition, the ternary complex also serves as a surveillance point, whereas incorrect uL14 is retained on Rkm1 and prevented from loading to the pre-60S ribosomal subunits. This study reveals the molecular mechanism of how uL14 is protected and quality checked by serial steps to ensure its safe delivery from the cytoplasm until its incorporation into the 60S ribosomal subunit.
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Affiliation(s)
- Min-Chi Yeh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ning-Hsiang Hsu
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Hao-Yu Chu
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jing-Ting Shie
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Wei-Ming Lee
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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2
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Chen P, Huang R, Hazbun TR. Unlocking the Mysteries of Alpha-N-Terminal Methylation and its Diverse Regulatory Functions. J Biol Chem 2023:104843. [PMID: 37209820 PMCID: PMC10293735 DOI: 10.1016/j.jbc.2023.104843] [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: 08/17/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Protein post-translation modifications (PTMs) are a critical regulatory mechanism of protein function. Protein α-N-terminal (Nα) methylation is a conserved PTM across prokaryotes and eukaryotes. Studies of the Nα methyltransferases responsible for Να methylation and their substrate proteins have shown that the PTM involves diverse biological processes, including protein synthesis and degradation, cell division, DNA damage response, and transcription regulation. This review provides an overview of the progress toward the regulatory function of Να methyltransferases and their substrate landscape. More than 200 proteins in humans and 45 in yeast are potential substrates for protein Nα methylation based on the canonical recognition motif, XP[KR]. Based on recent evidence for a less stringent motif requirement, the number of substrates might be increased, but further validation is needed to solidify this concept. A comparison of the motif in substrate orthologs in selected eukaryotic species indicates intriguing gain and loss of the motif across the evolutionary landscape. We discuss the state of knowledge in the field that has provided insights into the regulation of protein Να methyltransferases and their role in cellular physiology and disease. We also outline the current research tools that are key to understanding Να methylation. Finally, challenges are identified and discussed that would aid in unlocking a system-level view of the roles of Να methylation in diverse cellular pathways.
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Affiliation(s)
- Panyue Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tony R Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.
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3
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Nakamura R, Nakayama JI. Regulation of the SUV39H Family Methyltransferases: Insights from Fission Yeast. Biomolecules 2023; 13:biom13040593. [PMID: 37189341 DOI: 10.3390/biom13040593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Histones, which make up nucleosomes, undergo various post-translational modifications, such as acetylation, methylation, phosphorylation, and ubiquitylation. In particular, histone methylation serves different cellular functions depending on the location of the amino acid residue undergoing modification, and is tightly regulated by the antagonistic action of histone methyltransferases and demethylases. The SUV39H family of histone methyltransferases (HMTases) are evolutionarily conserved from fission yeast to humans and play an important role in the formation of higher-order chromatin structures called heterochromatin. The SUV39H family HMTases catalyzes the methylation of histone H3 lysine 9 (H3K9), and this modification serves as a binding site for heterochromatin protein 1 (HP1) to form a higher-order chromatin structure. While the regulatory mechanism of this family of enzymes has been extensively studied in various model organisms, Clr4, a fission yeast homologue, has made an important contribution. In this review, we focus on the regulatory mechanisms of the SUV39H family of proteins, in particular, the molecular mechanisms revealed by the studies of the fission yeast Clr4, and discuss their generality in comparison to other HMTases.
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4
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Grunchec H, Deraze J, Dardalhon-Cuménal D, Ribeiro V, Coléno-Costes A, Dias K, Bloyer S, Mouchel-Vielh E, Peronnet F, Thomassin H. Single amino-acid mutation in a Drosoph ila melanogaster ribosomal protein: An insight in uL11 transcriptional activity. PLoS One 2022; 17:e0273198. [PMID: 35981051 PMCID: PMC9387862 DOI: 10.1371/journal.pone.0273198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/04/2022] [Indexed: 11/26/2022] Open
Abstract
The ribosomal protein uL11 is located at the basis of the ribosome P-stalk and plays a paramount role in translational efficiency. In addition, no mutant for uL11 is available suggesting that this gene is haplo-insufficient as many other Ribosomal Protein Genes (RPGs). We have previously shown that overexpression of Drosophila melanogaster uL11 enhances the transcription of many RPGs and Ribosomal Biogenesis genes (RiBis) suggesting that uL11 might globally regulate the level of translation through its transcriptional activity. Moreover, uL11 trimethylated on lysine 3 (uL11K3me3) interacts with the chromodomain of the Enhancer of Polycomb and Trithorax Corto, and both proteins co-localize with RNA Polymerase II at many sites on polytene chromosomes. These data have led to the hypothesis that the N-terminal end of uL11, and more particularly the trimethylation of lysine 3, supports the extra-ribosomal activity of uL11 in transcription. To address this question, we mutated the lysine 3 codon using a CRISPR/Cas9 strategy and obtained several lysine 3 mutants. We describe here the first mutants of D. melanogaster uL11. Unexpectedly, the uL11K3A mutant, in which the lysine 3 codon is replaced by an alanine, displays a genuine Minute phenotype known to be characteristic of RPG deletions (longer development, low fertility, high lethality, thin and short bristles) whereas the uL11K3Y mutant, in which the lysine 3 codon is replaced by a tyrosine, is unaffected. In agreement, the rate of translation decreases in uL11K3A but not in uL11K3Y. Co-immunoprecipitation experiments show that the interaction between uL11 and the Corto chromodomain is impaired by both mutations. However, Histone Association Assays indicate that the mutant proteins still bind chromatin. RNA-seq analyses from wing imaginal discs show that Corto represses RPG expression whereas very few genes are deregulated in uL11 mutants. We propose that Corto, by repressing RPG expression, ensures that all ribosomal proteins are present at the correct stoichiometry, and that uL11 fine-tunes its transcriptional regulation of RPGs.
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Affiliation(s)
- Héloïse Grunchec
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Jérôme Deraze
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Delphine Dardalhon-Cuménal
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Valérie Ribeiro
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Anne Coléno-Costes
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Karine Dias
- Genomics Core Facility, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, Inserm, Université PSL, Paris, France
| | - Sébastien Bloyer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emmanuèle Mouchel-Vielh
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Frédérique Peronnet
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Hélène Thomassin
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
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5
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Dong C, Nakagawa R, Oyama K, Yamamoto Y, Zhang W, Dong A, Li Y, Yoshimura Y, Kamiya H, Nakayama JI, Ueda J, Min J. Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. eLife 2020; 9:58675. [PMID: 32869745 PMCID: PMC7492083 DOI: 10.7554/elife.58675] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/29/2020] [Indexed: 12/30/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a multicomponent histone H3K27 methyltransferase complex, best known for silencing the Hox genes during embryonic development. The Polycomb-like proteins PHF1, MTF2, and PHF19 are critical components of PRC2 by stimulating its catalytic activity in embryonic stem cells. The Tudor domains of PHF1/19 have been previously shown to be readers of H3K36me3 in vitro. However, some other studies suggest that PHF1 and PHF19 co-localize with the H3K27me3 mark but not H3K36me3 in cells. Here, we provide further evidence that PHF1 co-localizes with H3t in testis and its Tudor domain preferentially binds to H3tK27me3 over canonical H3K27me3 in vitro. Our complex structures of the Tudor domains of PHF1 and PHF19 with H3tK27me3 shed light on the molecular basis for preferential recognition of H3tK27me3 by PHF1 and PHF19 over canonical H3K27me3, implicating that H3tK27me3 might be a physiological ligand of PHF1/19.
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Affiliation(s)
- Cheng Dong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Reiko Nakagawa
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kyohei Oyama
- Department of Cardiac Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Yusuke Yamamoto
- Department of Cardiac Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Weilian Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan
| | - Hiroyuki Kamiya
- Department of Cardiac Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Jun Ueda
- Centre for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Canada
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6
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Oya E, Nakagawa R, Yoshimura Y, Tanaka M, Nishibuchi G, Machida S, Shirai A, Ekwall K, Kurumizaka H, Tagami H, Nakayama J. H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin assembly. EMBO Rep 2019; 20:e48111. [PMID: 31468675 PMCID: PMC6776926 DOI: 10.15252/embr.201948111] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 12/28/2022] Open
Abstract
The methylation of histone H3 at lysine 9 (H3K9me), performed by the methyltransferase Clr4/SUV39H, is a key event in heterochromatin assembly. In fission yeast, Clr4, together with the ubiquitin E3 ligase Cul4, forms the Clr4 methyltransferase complex (CLRC), whose physiological targets and biological role are currently unclear. Here, we show that CLRC-dependent H3 ubiquitylation regulates Clr4's methyltransferase activity. Affinity-purified CLRC ubiquitylates histone H3, and mass spectrometric and mutation analyses reveal that H3 lysine 14 (H3K14) is the preferred target of the complex. Chromatin immunoprecipitation analysis shows that H3K14 ubiquitylation (H3K14ub) is closely associated with H3K9me-enriched chromatin. Notably, the CLRC-mediated H3 ubiquitylation promotes H3K9me by Clr4, suggesting that H3 ubiquitylation is intimately linked to the establishment and/or maintenance of H3K9me. These findings demonstrate a cross-talk mechanism between histone ubiquitylation and methylation that is involved in heterochromatin assembly.
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Affiliation(s)
- Eriko Oya
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Present address:
Faculty of Science and EngineeringChuo UniversityBunkyo‐ku, TokyoJapan
| | - Reiko Nakagawa
- Laboratory for PhyloinformaticsRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Yuriko Yoshimura
- Division of Chromatin RegulationNational Institute for Basic BiologyOkazakiJapan
| | - Mayo Tanaka
- Division of Chromatin RegulationNational Institute for Basic BiologyOkazakiJapan
| | - Gohei Nishibuchi
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
- Present address:
Graduate School of ScienceOsaka UniversityToyonakaJapan
| | - Shinichi Machida
- Laboratory of Structural BiologyGraduate School of Advanced Science and EngineeringWaseda UniversityShinjuku‐ku, TokyoJapan
- Present address:
Institute of Human GeneticsCNRS UMR 9002MontpellierFrance
| | | | - Karl Ekwall
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Hitoshi Kurumizaka
- Laboratory of Structural BiologyGraduate School of Advanced Science and EngineeringWaseda UniversityShinjuku‐ku, TokyoJapan
- Laboratory of Chromatin Structure and FunctionInstitute for Quantitative BiosciencesThe University of TokyoBunkyo‐ku, TokyoJapan
| | - Hideaki Tagami
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
| | - Jun‐ichi Nakayama
- Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
- Division of Chromatin RegulationNational Institute for Basic BiologyOkazakiJapan
- Department of Basic BiologySchool of Life ScienceThe Graduate University for Advanced Studies (SOKENDAI)OkazakiJapan
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7
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Shen Y, Mevius DE, Caliandro R, Carrozzini B, Roh Y, Kim J, Kim S, Ha SC, Morishita M, di Luccio E. Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis. Structure 2019; 27:631-638.e8. [DOI: 10.1016/j.str.2019.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/23/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022]
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8
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Sakai R, Fukuda R, Unida S, Aki M, Ono Y, Endo A, Kusumi S, Koga D, Fukushima T, Komada M, Okiyoneda T. The integral function of the endocytic recycling compartment is regulated by RFFL-mediated ubiquitylation of Rab11 effectors. J Cell Sci 2019; 132:jcs.228007. [PMID: 30659120 DOI: 10.1242/jcs.228007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022] Open
Abstract
Endocytic trafficking is regulated by ubiquitylation (also known as ubiquitination) of cargoes and endocytic machineries. The role of ubiquitylation in lysosomal delivery has been well documented, but its role in the recycling pathway is largely unknown. Here, we report that the ubiquitin (Ub) ligase RFFL regulates ubiquitylation of endocytic recycling regulators. An RFFL dominant-negative (DN) mutant induced clustering of endocytic recycling compartments (ERCs) and delayed endocytic cargo recycling without affecting lysosomal traffic. A BioID RFFL interactome analysis revealed that RFFL interacts with the Rab11 effectors EHD1, MICALL1 and class I Rab11-FIPs. The RFFL DN mutant strongly captured these Rab11 effectors and inhibited their ubiquitylation. The prolonged interaction of RFFL with Rab11 effectors was sufficient to induce the clustered ERC phenotype and to delay cargo recycling. RFFL directly ubiquitylates these Rab11 effectors in vitro, but RFFL knockout (KO) only reduced the ubiquitylation of Rab11-FIP1. RFFL KO had a minimal effect on the ubiquitylation of EHD1, MICALL1, and Rab11-FIP2, and failed to delay transferrin recycling. These results suggest that multiple Ub ligases including RFFL regulate the ubiquitylation of Rab11 effectors, determining the integral function of the ERC.
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Affiliation(s)
- Ryohei Sakai
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Shin Unida
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Misaki Aki
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Yuji Ono
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
| | - Akinori Endo
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Kusumi
- Division of Morphological Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Daisuke Koga
- Department of Microscopic Anatomy and Cell Biology, Asahikawa Medical University, Asahikawa 078-8510, Hokkaido, Japan
| | - Toshiaki Fukushima
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masayuki Komada
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Tsukasa Okiyoneda
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo 669-1337, Japan
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9
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Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nat Ecol Evol 2018; 2:1761-1771. [PMID: 30297745 DOI: 10.1038/s41559-018-0673-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/16/2018] [Indexed: 02/07/2023]
Abstract
Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8-6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates.
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10
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Okazaki K, Kato H, Iida T, Shinmyozu K, Nakayama JI, Murakami Y, Urano T. RNAi-dependent heterochromatin assembly in fission yeast Schizosaccharomyces pombe requires heat-shock molecular chaperones Hsp90 and Mas5. Epigenetics Chromatin 2018; 11:26. [PMID: 29866182 PMCID: PMC5985592 DOI: 10.1186/s13072-018-0199-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/31/2018] [Indexed: 11/28/2022] Open
Abstract
Background Heat-shock molecular chaperone proteins (Hsps) promote the loading of small interfering RNA (siRNA) onto RNA interference (RNAi) effector complexes. While the RNAi process is coupled with heterochromatin assembly in several model organisms, it remains unclear whether the Hsps contribute to epigenetic gene regulation. In this study, we used the fission yeast Schizosaccharomyces pombe as a model organism and investigated the roles of Hsp90 and Mas5 (a nucleocytoplasmic type-I Hsp40 protein) in RNAi-dependent heterochromatin assembly. Results Using a genetic screen and biochemical analyses, we identified Hsp90 and Mas5 as novel silencing factors. Mutations in the genes encoding these factors caused derepression of silencing at the pericentromere, where heterochromatin is assembled in an RNAi-dependent manner, but not at the subtelomere, where RNAi is dispensable. The mutations also caused a substantial reduction in the level of dimethylation of histone H3 at Lys9 at the pericentromere, where association of the Argonaute protein Ago1 was also abrogated. Consistently, siRNA corresponding to the pericentromeric repeats was undetectable in these mutant cells. In addition, levels of Tas3, which is a protein in the RNA-induced transcriptional silencing complex along with Ago1, were reduced in the absence of Mas5. Conclusions Our results suggest that the Hsps Hsp90 and Mas5 contribute to RNAi-dependent heterochromatin assembly. In particular, Mas5 appears to be required to stabilize Tas3 in vivo. We infer that impairment of Hsp90 and Hsp40 also may affect the integrity of the epigenome in other organisms. Electronic supplementary material The online version of this article (10.1186/s13072-018-0199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kosuke Okazaki
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.,KNC Laboratories Co. Ltd., Kobe, Hyogo, 651-2271, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Tetsushi Iida
- Division of Cytogenetics, National Institute of Genetics, Mishima, 1111 Yata, Mishima, 411-8540, Japan.,Laboratory for Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Kaori Shinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo, 650-0047, Japan.,National Cerebral and Cardiovascular Center, Suita, Osaka, 565-8565, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
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11
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Clarke SG. The ribosome: A hot spot for the identification of new types of protein methyltransferases. J Biol Chem 2018; 293:10438-10446. [PMID: 29743234 DOI: 10.1074/jbc.aw118.003235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cellular physiology depends on the alteration of protein structures by covalent modification reactions. Using a combination of bioinformatic, genetic, biochemical, and mass spectrometric approaches, it has been possible to probe ribosomal proteins from the yeast Saccharomyces cerevisiae for post-translationally methylated amino acid residues and for the enzymes that catalyze these modifications. These efforts have resulted in the identification and characterization of the first protein histidine methyltransferase, the first N-terminal protein methyltransferase, two unusual types of protein arginine methyltransferases, and a new type of cysteine methylation. Two of these enzymes may modify their substrates during ribosomal assembly because the final methylated histidine and arginine residues are buried deep within the ribosome with contacts only with RNA. Two of these modifications occur broadly in eukaryotes, including humans, whereas the others demonstrate a more limited phylogenetic range. Analysis of strains where the methyltransferase genes are deleted has given insight into the physiological roles of these modifications. These reactions described here add diversity to the modifications that generate the typical methylated lysine and arginine residues previously described in histones and other proteins.
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Affiliation(s)
- Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095
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12
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Hatakeyama D, Shoji M, Yamayoshi S, Yoh R, Ohmi N, Takenaka S, Saitoh A, Arakaki Y, Masuda A, Komatsu T, Nagano R, Nakano M, Noda T, Kawaoka Y, Kuzuhara T. Influenza A virus nucleoprotein is acetylated by histone acetyltransferases PCAF and GCN5. J Biol Chem 2018; 293:7126-7138. [PMID: 29555684 PMCID: PMC5950015 DOI: 10.1074/jbc.ra117.001683] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/09/2018] [Indexed: 12/22/2022] Open
Abstract
Histone acetylation plays crucial roles in transcriptional regulation and chromatin organization. Viral RNA of the influenza virus interacts with its nucleoprotein (NP), whose function corresponds to that of eukaryotic histones. NP regulates viral replication and has been shown to undergo acetylation by the cAMP-response element (CRE)–binding protein (CBP) from the host. However, whether NP is the target of other host acetyltransferases is unknown. Here, we show that influenza virus NP undergoes acetylation by the two host acetyltransferases GCN5 and P300/CBP-associated factor (PCAF) and that this modification affects viral polymerase activities. Western blot analysis with anti–acetyl-lysine antibody on cultured A549 human lung adenocarcinoma epithelial cells infected with different influenza virus strains indicated acetylation of the viral NP. A series of biochemical analyses disclosed that the host lysine acetyltransferases GCN5 and PCAF acetylate NP in vitro. MS experiments identified three lysine residues as acetylation targets in the host cells and suggested that Lys-31 and Lys-90 are acetylated by PCAF and GCN5, respectively. RNAi-mediated silencing of GCN5 and PCAF did not change acetylation levels of NP. However, interestingly, viral polymerase activities were increased by the PCAF silencing and were decreased by the GCN5 silencing, suggesting that acetylation of the Lys-31 and Lys-90 residues has opposing effects on viral replication. Our findings suggest that epigenetic control of NP via acetylation by host acetyltransferases contributes to regulation of polymerase activity in the influenza A virus.
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Affiliation(s)
- Dai Hatakeyama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Masaki Shoji
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Rina Yoh
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Naho Ohmi
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Shiori Takenaka
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Ayaka Saitoh
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Yumie Arakaki
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Aki Masuda
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Tsugunori Komatsu
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Rina Nagano
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Masahiro Nakano
- Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Takeshi Noda
- Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan; PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53711
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan.
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13
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Kozel C, Thompson B, Hustak S, Moore C, Nakashima A, Singh CR, Reid M, Cox C, Papadopoulos E, Luna RE, Anderson A, Tagami H, Hiraishi H, Slone EA, Yoshino KI, Asano M, Gillaspie S, Nietfeld J, Perchellet JP, Rothenburg S, Masai H, Wagner G, Beeser A, Kikkawa U, Fleming SD, Asano K. Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation. Nucleic Acids Res 2016; 44:8704-8713. [PMID: 27325740 PMCID: PMC5062967 DOI: 10.1093/nar/gkw559] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 11/14/2022] Open
Abstract
ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby promoting translation of GCN4, the yeast ATF4 equivalent. Furthermore, regulatory protein termed eIF5-mimic protein (5MP) can bind eIF2 and inhibit general translation. Here, we show that 5MP1 overexpression in human cells leads to strong formation of 5MP1:eIF2 complex, nearly comparable to that of eIF5:eIF2 complex produced by eIF5 overexpression. Overexpression of eIF5, 5MP1 and 5MP2, the second human paralog, promotes ATF4 expression in certain types of human cells including fibrosarcoma. 5MP overexpression also induces ATF4 expression in Drosophila The knockdown of 5MP1 in fibrosarcoma attenuates ATF4 expression and its tumor formation on nude mice. Since 5MP2 is overproduced in salivary mucoepidermoid carcinoma, we propose that overexpression of eIF5 and 5MP induces translation of ATF4 and potentially other genes with uORFs in their mRNA leaders through delayed re-initiation, thereby enhancing the survival of normal and cancer cells under stress conditions.
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Affiliation(s)
- Caitlin Kozel
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Brytteny Thompson
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Samantha Hustak
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Chelsea Moore
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Akio Nakashima
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | - Chingakham Ranjit Singh
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Megan Reid
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Christian Cox
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Evangelos Papadopoulos
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rafael E Luna
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Abbey Anderson
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
| | - Hiroyuki Hiraishi
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Emily Archer Slone
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ken-Ichi Yoshino
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | - Masayo Asano
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Sarah Gillaspie
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Jerome Nietfeld
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Jean-Pierre Perchellet
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Stefan Rothenburg
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Hisao Masai
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Beeser
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ushio Kikkawa
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | - Sherry D Fleming
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Katsura Asano
- Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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14
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Mevius DEHF, Shen Y, Morishita M, di Luccio E. Cloning, expression, purification and crystallization of Schizosaccharomyces pombe Set7, a putative histone methyltransferase. Acta Crystallogr F Struct Biol Commun 2016; 72:263-8. [PMID: 27050258 PMCID: PMC4822981 DOI: 10.1107/s2053230x16003794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/06/2016] [Indexed: 11/11/2022] Open
Abstract
Dysfunction of histone-modifying enzymes affects chromatin regulation and is involved in carcinogenesis, tumour progression and other diseases. Histone methyltransferases are a family of key histone-modifying enzymes, but their structures, functions and mechanisms are incompletely understood, thus constraining drug-design efforts. Here, preliminary steps towards structure-function studies of Schizosaccharomyces pombe Set7, a putative histone methyltransferase and the first yeast full-length SET-domain-containing protein to be studied using X-ray crystallography, are reported. The methods from cloning to X-ray diffraction and phasing are discussed and the results will aid in prospective studies of histone-modifying enzymes.
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Affiliation(s)
- Damiaan E. H. F. Mevius
- Genetic Engineering Department, School of Life Sciences, College of Natural Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Food Biomaterials, College of Agriculture and Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Yunpeng Shen
- Genetic Engineering Department, School of Life Sciences, College of Natural Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Food Biomaterials, College of Agriculture and Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Masayo Morishita
- Genetic Engineering Department, School of Life Sciences, College of Natural Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Eric di Luccio
- Genetic Engineering Department, School of Life Sciences, College of Natural Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
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15
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Cai Q, Fu L, Wang Z, Gan N, Dai X, Wang Y. α-N-methylation of damaged DNA-binding protein 2 (DDB2) and its function in nucleotide excision repair. J Biol Chem 2014; 289:16046-56. [PMID: 24753253 DOI: 10.1074/jbc.m114.558510] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DDB2 exhibits a high affinity toward UV-damaged DNA, and it is involved in the initial steps of global genome nucleotide excision repair. Mutations in the DDB2 gene cause the genetic complementation group E of xeroderma pigmentosum, an autosomal recessive disease manifested clinically by hypersensitivity to sunlight exposure and an increased predisposition to skin cancer. Here we found that, in human cells, the initiating methionine residue in DDB2 was removed and that the N-terminal alanine could be methylated on its α-amino group in human cells, with trimethylation being the major form. We also demonstrated that the α-N-methylation of DDB2 is catalyzed by the N-terminal RCC1 methyltransferase. In addition, a methylation-defective mutant of DDB2 displayed diminished nuclear localization and was recruited at a reduced efficiency to UV-induced cyclobutane pyrimidine dimer foci. Moreover, loss of this methylation conferred compromised ATM (ataxia telangiectasia mutated) activation, decreased efficiency in cyclobutane pyrimidine dimer repair, and elevated sensitivity of cells toward UV light exposure. Our study provides new knowledge about the posttranslational regulation of DDB2 and expands the biological functions of protein α-N-methylation to DNA repair.
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Affiliation(s)
- Qian Cai
- From the Environmental Toxicology Graduate Program and
| | - Lijuan Fu
- From the Environmental Toxicology Graduate Program and
| | - Zi Wang
- From the Environmental Toxicology Graduate Program and
| | - Nanqin Gan
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Yinsheng Wang
- From the Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521-0403
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16
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Lanouette S, Mongeon V, Figeys D, Couture JF. The functional diversity of protein lysine methylation. Mol Syst Biol 2014; 10:724. [PMID: 24714364 PMCID: PMC4023394 DOI: 10.1002/msb.134974] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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17
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Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochem Biophys Res Commun 2014; 445:535-41. [PMID: 24486316 DOI: 10.1016/j.bbrc.2014.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023]
Abstract
Ribosomes, as the center of protein translation in the cell, require careful regulation via multiple pathways. While regulation of ribosomal synthesis and function has been widely studied on the transcriptional and translational "levels," the biological roles of ribosomal post-translational modifications (PTMs) are largely not understood. Here, we explore this matter by using quantitative mass spectrometry to compare the prevalence of ribosomal methylation and acetylation for yeast in the log phase and the stationary phase of growth. We find that of the 27 modified peptides identified, two peptides experience statistically significant changes in abundance: a 1.9-fold decrease in methylation for k(Me)VSGFKDEVLETV of ribosomal protein S1B (RPS1B), and a 10-fold increase in dimethylation for r(DiMe)GGFGGR of ribosomal protein S2 (RPS2). While the biological role of RPS1B methylation has largely been unexplored, RPS2 methylation is a modification known to have a role in processing and export of ribosomal RNA. This suggests that yeast in the stationary phase increase methylation of RPS2 in order to regulate ribosomal synthesis. These results demonstrate the utility of mass spectrometry for quantifying dynamic changes in ribosomal PTMs.
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Affiliation(s)
- Daniel T Ladror
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark E Levenstein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Jacklyn M Artymiuk
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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18
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Kamata K, Goswami G, Kashio S, Urano T, Nakagawa R, Uchida H, Oki M. The N-terminus and Tudor domains of Sgf29 are important for its heterochromatin boundary formation function. ACTA ACUST UNITED AC 2013; 155:159-71. [DOI: 10.1093/jb/mvt108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Dai X, Otake K, You C, Cai Q, Wang Z, Masumoto H, Wang Y. Identification of novel α-n-methylation of CENP-B that regulates its binding to the centromeric DNA. J Proteome Res 2013; 12:4167-75. [PMID: 23978223 DOI: 10.1021/pr400498y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic centromere is an essential chromatin region required for accurate segregation of sister chromatids during cell division. Centromere protein B (CENP-B) is a highly conserved protein which can bind to the 17-bp CENP-B box on the centromeric DNA. In this study, we found that CENP-B could be α-N-methylated in human cells. We also showed that the level of the α-N-methylation was stimulated in cells in response to a variety of extracellular stimuli, including increased cell density, heat shock, and arsenite treatment, although the methylation level was not altered upon metaphase arrest. We identified N-terminal RCC1 methyltransferase (NRMT) as a major enzyme required for the CENP-B methylation. Additionally, we found that chromatin-bound CENP-B was primarily trimethylated and α-N-trimethylation could enhance CENP-B's binding to CENP-B box in cells. Our study also expands the function of protein α-N-methylation that has been known for decades and whose function remains largely unexplored.
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Affiliation(s)
- Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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20
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Kamata K, Hatanaka A, Goswami G, Shinmyozu K, Nakayama JI, Urano T, Hatashita M, Uchida H, Oki M. C-terminus of the Sgf73 subunit of SAGA and SLIK is important for retention in the larger complex and for heterochromatin boundary function. Genes Cells 2013; 18:823-37. [DOI: 10.1111/gtc.12075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/22/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Kazuma Kamata
- Department of Applied Chemistry & Biotechnology; Graduate School of Engineering; University of Fukui; Fukui 910-8507; Japan
| | - Akira Hatanaka
- Department of Applied Chemistry & Biotechnology; Graduate School of Engineering; University of Fukui; Fukui 910-8507; Japan
| | - Gayatri Goswami
- Department of Applied Chemistry & Biotechnology; Graduate School of Engineering; University of Fukui; Fukui 910-8507; Japan
| | - Kaori Shinmyozu
- Center for Developmental Biology; Laboratory for Chromatin Dynamics; RIKEN; Kobe 650-0047; Japan
| | | | - Takeshi Urano
- Department of Biochemistry; Shimane University Faculty of Medicine; Izumo 693-8501; Japan
| | - Masanori Hatashita
- Research and Development Department; Wakasa Wan Energy Research Center; Tsuruga 914-0192; Japan
| | - Hiroyuki Uchida
- Department of Applied Chemistry & Biotechnology; Graduate School of Engineering; University of Fukui; Fukui 910-8507; Japan
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21
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Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F. New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain. PLoS Genet 2012; 8:e1003006. [PMID: 23071455 PMCID: PMC3469418 DOI: 10.1371/journal.pgen.1003006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/16/2012] [Indexed: 01/24/2023] Open
Abstract
Chromodomains are found in many regulators of chromatin structure, and most of them recognize methylated lysines on histones. Here, we investigate the role of the Drosophila melanogaster protein Corto's chromodomain. The Enhancer of Trithorax and Polycomb Corto is involved in both silencing and activation of gene expression. Over-expression of the Corto chromodomain (CortoCD) in transgenic flies shows that it is a chromatin-targeting module, critical for Corto function. Unexpectedly, mass spectrometry analysis reveals that polypeptides pulled down by CortoCD from nuclear extracts correspond to ribosomal proteins. Furthermore, real-time interaction analyses demonstrate that CortoCD binds with high affinity RPL12 tri-methylated on lysine 3. Corto and RPL12 co-localize with active epigenetic marks on polytene chromosomes, suggesting that both are involved in fine-tuning transcription of genes in open chromatin. RNA-seq based transcriptomes of wing imaginal discs over-expressing either CortoCD or RPL12 reveal that both factors deregulate large sets of common genes, which are enriched in heat-response and ribosomal protein genes, suggesting that they could be implicated in dynamic coordination of ribosome biogenesis. Chromatin immunoprecipitation experiments show that Corto and RPL12 bind hsp70 and are similarly recruited on gene body after heat shock. Hence, Corto and RPL12 could be involved together in regulation of gene transcription. We discuss whether pseudo-ribosomal complexes composed of various ribosomal proteins might participate in regulation of gene expression in connection with chromatin regulators.
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Affiliation(s)
- Anne Coléno-Costes
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Suk Min Jang
- Institut Pasteur, Département de Biologie du Développement, Unité de Régulation Epigénétique, Paris, France
- Centre National de la Recherche Scientifique, URA2578, Paris, France
- INSERM Avenir, Paris, France
| | - Augustin de Vanssay
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Répression Épigénétique et Éléments Transposables, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Répression Épigénétique et Éléments Transposables, Paris, France
| | - Julien Rougeot
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Tahar Bouceba
- Plateforme d'Ingénierie des Protéines, Service d'Interaction des Biomolécules, IFR83, Université Pierre et Marie Curie-Paris 6, UMR7622, Paris, France
| | - Neel B. Randsholt
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Jean-Michel Gibert
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Stéphane Le Crom
- École Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Plateforme Génomique, Paris, France
- INSERM, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Analyse des Données à Haut Débit en Génomique Fonctionnelle, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Analyse des Données à Haut Débit en Génomique Fonctionnelle, Paris, France
| | - Emmanuèle Mouchel-Vielh
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Sébastien Bloyer
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Frédérique Peronnet
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
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22
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Zhang Q, van der Donk WA. Catalytic promiscuity of a bacterial α-N-methyltransferase. FEBS Lett 2012; 586:3391-7. [PMID: 22841713 PMCID: PMC3462432 DOI: 10.1016/j.febslet.2012.07.050] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/12/2012] [Accepted: 07/13/2012] [Indexed: 11/28/2022]
Abstract
The posttranslational methylation of N-terminal α-amino groups (α-N-methylation) is a ubiquitous reaction found in all domains of life. Although this modification usually occurs on protein substrates, recent studies have shown that it also takes place on ribosomally synthesized natural products. Here we report an investigation of the bacterial α-N-methyltransferase CypM involved in the biosynthesis of the peptide antibiotic cypemycin. We demonstrate that CypM has low substrate selectivity and methylates a variety of oligopeptides, cyclic peptides such as nisin and haloduracin, and the ε-amino group of lysine. Hence it may have potential for enzyme engineering and combinatorial biosynthesis. Bayesian phylogenetic inference of bacterial α-N-methyltransferases suggests that they have not evolved as a specific group based on the chemical transformations they catalyze, but that they have been acquired from various other methyltransferase classes during evolution.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 161 Roger Adams Laboratory, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 161 Roger Adams Laboratory, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Hatanaka A, Chen B, Sun JQ, Mano Y, Funakoshi M, Kobayashi H, Ju Y, Mizutani T, Shinmyozu K, Nakayama JI, Miyamoto K, Uchida H, Oki M. Fub1p, a novel protein isolated by boundary screening, binds the proteasome complex. Genes Genet Syst 2012; 86:305-14. [PMID: 22362029 DOI: 10.1266/ggs.86.305] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Silenced chromatin domains are restricted to specific regions. Eukaryotic chromosomes are organized into discrete domains delimited by domain boundaries. From approximately 6,000 genes in Saccharomyces cerevisiae, we previously isolated 55 boundary genes. In this study, we focus on the molecular function of one of boundary genes, YCR076C/FUB1 (function of boundary), whose function has not been clearly defined in vivo. Biochemical analysis of Fub1p revealed that it interacted with multiple subunits of the 20S proteasome core particle (20S CP). To further clarify the functional link between Fub1p and proteasome, several proteasome mutants were analyzed. Although only 20S CP subunits were isolated as Fub1p interactors, a genetic interaction was also observed for component of 19S regulatory particle (19S RP) suggesting involvement of Fub1p with the whole proteasome. We also analyzed the mechanism of boundary establishment by using proteasome composition factor-deficient strains. Deletion of pre9 and ump1, whose products have effects on the 20S CP, resulted in a decrease in boundary function. Domain analyses of Fub1p identified a minimum functional domain in the C terminus that was essential for boundary establishment and showed a limited sequence homology to the human PSMF1, which is known to inhibit proteasome activity. Finally, boundary assay showed that human PSMF1 also exhibited boundary establishment activity in yeast. Our results defined the functional correlation between Fub1p and PSMF1.
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Affiliation(s)
- Akira Hatanaka
- Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
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24
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Erce MA, Pang CNI, Hart-Smith G, Wilkins MR. The methylproteome and the intracellular methylation network. Proteomics 2012; 12:564-86. [DOI: 10.1002/pmic.201100397] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/23/2011] [Accepted: 10/17/2011] [Indexed: 12/30/2022]
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25
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Zou P, Yoshihara H, Hosokawa K, Tai I, Shinmyozu K, Tsukahara F, Maru Y, Nakayama K, Nakayama KI, Suda T. p57(Kip2) and p27(Kip1) cooperate to maintain hematopoietic stem cell quiescence through interactions with Hsc70. Cell Stem Cell 2011; 9:247-61. [PMID: 21885020 DOI: 10.1016/j.stem.2011.07.003] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 02/15/2011] [Accepted: 07/07/2011] [Indexed: 01/03/2023]
Abstract
Cell cycle regulators play critical roles in the balance between hematopoietic stem cell (HSC) dormancy and proliferation. In this study, we report that cell cycle entry proceeded normally in HSCs null for cyclin-dependent kinase (CDK) inhibitor p57 due to compensatory upregulation of p27. HSCs null for both p57 and p27, however, were more proliferative and had reduced capacity to engraft in transplantation. We found that heat shock cognate protein 70 (Hsc70) interacts with both p57 and p27 and that the subcellular localization of Hsc70 was critical to maintain HSC cell cycle kinetics. Combined deficiency of p57 and p27 in HSCs resulted in nuclear import of an Hsc70/cyclin D1 complex, concomitant with Rb phosphorylation, and elicited severe defects in maintaining HSC quiescence. Taken together, these data suggest that regulation of cytoplasmic localization of Hsc70/cyclin D1 complex by p57 and p27 is a key intracellular mechanism in controlling HSC dormancy.
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Affiliation(s)
- Peng Zou
- Department of Cell Differentiation, The Sakaguchi Laboratory of Developmental Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
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26
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Kitano E, Hayashi A, Kanai D, Shinmyozu K, Nakayama JI. Roles of fission yeast Grc3 protein in ribosomal RNA processing and heterochromatic gene silencing. J Biol Chem 2011; 286:15391-402. [PMID: 21385875 PMCID: PMC3083176 DOI: 10.1074/jbc.m110.201343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 03/01/2011] [Indexed: 01/26/2023] Open
Abstract
Grc3 is an evolutionarily conserved protein. Genome-wide budding yeast studies suggest that Grc3 is involved in rRNA processing. In the fission yeast Schizosaccharomyces pombe, Grc3 was identified as a factor exhibiting distinct nuclear dot localization, yet its exact physiological function remains unknown. Here, we show that S. pombe Grc3 is required for both rRNA processing and heterochromatic gene silencing. Cytological analysis revealed that Grc3 nuclear dots correspond to heterochromatic regions and that some Grc3 is also present in the nucleolar peripheral region. Depleting the heterochromatic proteins Swi6 or Clr4 abolished heterochromatic localization of Grc3 and resulted in its preferential accumulation in the perinucleolar region, suggesting its dynamic association with these nuclear compartments. Cells expressing mutant grc3 showed defects in 25 S rRNA maturation and in heterochromatic gene silencing. Protein analysis of Grc3-containing complexes led to the identification of Las1 and components of the IPI complex (Rix1, Ipi1, and Crb3). All of these Grc3-interacting proteins showed a dynamic nuclear localization similar to that observed for Grc3, and those conditional mutants showed defects in both rRNA processing and silencing of centromeric transcripts. Our data suggest that Grc3 functions cooperatively with Las1 and the IPI complex in both ribosome biogenesis and heterochromatin assembly.
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Affiliation(s)
- Erina Kitano
- From the Laboratory for Chromatin Dynamics and
- the Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan, and
| | - Aki Hayashi
- From the Laboratory for Chromatin Dynamics and
| | - Daigo Kanai
- From the Laboratory for Chromatin Dynamics and
- the Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
| | - Kaori Shinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe Hyogo 650-0047, Japan
| | - Jun-ichi Nakayama
- From the Laboratory for Chromatin Dynamics and
- the Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
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27
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Webb KJ, Al-Hadid Q, Zurita-Lopez CI, Young BD, Lipson RS, Clarke SG. The ribosomal l1 protuberance in yeast is methylated on a lysine residue catalyzed by a seven-beta-strand methyltransferase. J Biol Chem 2011; 286:18405-13. [PMID: 21460220 DOI: 10.1074/jbc.m110.200410] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Modification of proteins of the translational apparatus is common in many organisms. In the yeast Saccharomyces cerevisiae, we provide evidence for the methylation of Rpl1ab, a well conserved protein forming the ribosomal L1 protuberance of the large subunit that functions in the release of tRNA from the exit site. We show that the intact mass of Rpl1ab is 14 Da larger than its calculated mass with the previously described loss of the initiator methionine residue and N-terminal acetylation. We determined that the increase in mass of yeast Rpl1ab is consistent with the addition of a methyl group to lysine 46 using top-down mass spectrometry. Lysine modification was confirmed by detecting (3)H-N-ε-monomethyllysine in hydrolysates of Rpl1ab purified from yeast cells radiolabeled in vivo with S-adenosyl-l-[methyl-(3)H]methionine. Mass spectrometric analysis of intact Rpl1ab purified from 37 deletion strains of known and putative yeast methyltransferases revealed that only the deletion of the YLR137W gene, encoding a seven-β-strand methyltransferase, results in the loss of the +14-Da modification. We expressed the YLR137W gene as a His-tagged protein in Escherichia coli and showed that it catalyzes N-ε-monomethyllysine formation within Rpl1ab on ribosomes from the ΔYLR137W mutant strain lacking the methyltransferase activity but not from wild-type ribosomes. We also showed that the His-tagged protein could catalyze monomethyllysine formation on a 16-residue peptide corresponding to residues 38-53 of Rpl1ab. We propose that the YLR137W gene be given the standard name RKM5 (ribosomal lysine (K) methyltransferase 5). Orthologs of RKM5 are found only in fungal species, suggesting a role unique to their survival.
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Affiliation(s)
- Kristofor J Webb
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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28
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Abstract
The phosphorylation of heterochromatin protein 1 (HP1) has been previously described in studies of mammals, but the biological implications of this modification remain largely elusive. Here, we show that the N-terminal phosphorylation of HP1α plays a central role in its targeting to chromatin. Recombinant HP1α prepared from mammalian cultured cells exhibited a stronger binding affinity for K9-methylated histone H3 (H3K9me) than that produced in Escherichia coli. Biochemical analyses revealed that HP1α was multiply phosphorylated at N-terminal serine residues (S11-14) in human and mouse cells and that this phosphorylation enhanced HP1α's affinity for H3K9me. Importantly, the N-terminal phosphorylation appeared to facilitate the initial binding of HP1α to H3K9me by mediating the interaction between HP1α and a part of the H3 tail that was distinct from the methylated K9. Unphosphorylatable mutant HP1α exhibited severe heterochromatin localization defects in vivo, and its prolonged expression led to increased chromosomal instability. Our results suggest that HP1α's N-terminal phosphorylation is essential for its proper targeting to heterochromatin and that its binding to the methylated histone tail is achieved by the cooperative action of the chromodomain and neighboring posttranslational modifications.
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29
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Aravind L, Abhiman S, Iyer LM. Natural history of the eukaryotic chromatin protein methylation system. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:105-76. [PMID: 21507350 DOI: 10.1016/b978-0-12-387685-0.00004-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In eukaryotes, methylation of nucleosomal histones and other nuclear proteins is a central aspect of chromatin structure and dynamics. The past 15 years have seen an enormous advance in our understanding of the biochemistry of these modifications, and of their role in establishing the epigenetic code. We provide a synthetic overview, from an evolutionary perspective, of the main players in the eukaryotic chromatin protein methylation system, with an emphasis on catalytic domains. Several components of the eukaryotic protein methylation system had their origins in bacteria. In particular, the Rossmann fold protein methylases (PRMTs and DOT1), and the LSD1 and jumonji-related demethylases and oxidases, appear to have emerged in the context of bacterial peptide methylation and hydroxylation systems. These systems were originally involved in synthesis of peptide secondary metabolites, such as antibiotics, toxins, and siderophores. The peptidylarginine deiminases appear to have been acquired by animals from bacterial enzymes that modify cell-surface proteins. SET domain methylases, which display the β-clip fold, apparently first emerged in prokaryotes from the SAF superfamily of carbohydrate-binding domains. However, even in bacteria, a subset of the SET domains might have evolved a chromatin-related role in conjunction with a BAF60a/b-like SWIB domain protein and topoisomerases. By the time of the last eukaryotic common ancestor, multiple SET and PRMT methylases were already in place and are likely to have mediated methylation at the H3K4, H3K9, H3K36, and H4K20 positions, and carried out both asymmetric and symmetric arginine dimethylation. Inference of H3K27 methylation in the ancestral eukaryote appears uncertain, though it was certainly in place a little later in eukaryotic evolution. Current data suggest that unlike SET methylases, which are universally present in eukaryotes, demethylases are not. They appear to be absent in the earliest-branching eukaryotic lineages, and emerged later along with several other chromatin proteins, such as the Dot1-methylase, prior to divergence of the kinetoplastid-heterolobosean lineage from the remaining eukaryotes. This period also corresponds to the point of origin of DNA cytosine methylation by DNMT1. Origin of major lineages of SET domains such as the Trithorax, Su(var)3-9, Ash1, SMYD, and TTLL12 and E(Z) might have played the initial role in the establishment of multiple distinct heterochromatic and euchromatic states that are likely to have been present, in some form, through much of eukaryotic evolution. Elaboration of these chromatin states might have gone hand-in-hand with acquisition of multiple jumonji-related and LSD1-like demethylases, and functional linkages with the DNA methylation and RNAi systems. Throughout eukaryotic evolution, there were several lineage-specific expansions of SET domain proteins, which might be related to a special transcription regulation process in trypanosomes, acquisition of new meiotic recombination hotspots in animals, and methylation and associated modifications of the diatom silaffin proteins involved in silica biomineralization. The use of specific domains to "read" the methylation marks appears to have been present in the ancestral eukaryote itself. Of these the chromo-like domains appear to have been acquired from bacterial secreted proteins that might have a role in binding cell-surface peptides or peptidoglycan. Domain architectures of the primary enzymes involved in the eukaryotic protein methylation system indicate key features relating to interactions with each other and other modifications in chromatin, such as acetylation. They also emphasize the profound functional distinction between the role of demethylation and deacetylation in regulation of chromatin dynamics.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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30
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Egorova KS, Olenkina OM, Olenina LV. Lysine methylation of nonhistone proteins is a way to regulate their stability and function. BIOCHEMISTRY (MOSCOW) 2010; 75:535-48. [PMID: 20632931 DOI: 10.1134/s0006297910050019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review is devoted to the dramatically expanding investigations of lysine methylation on nonhistone proteins and its functional importance. Posttranslational covalent modifications of proteins provide living organisms with ability to rapidly change protein activity and function in response to various stimuli. Enzymatic protein methylation at different lysine residues was evaluated in histones as a part of the "histone code". Histone methyltransferases methylate not only histones, but also many nuclear and cytoplasmic proteins. Recent data show that the regulatory role of lysine methylation on proteins is not restricted to the "histone code". This modification modulates activation, stabilization, and degradation of nonhistone proteins, thus influencing numerous cell processes. In this review we particularly focused on methylation of transcription factors and other nuclear nonhistone proteins. The methylated lysine residues serve as markers attracting nuclear "reader" proteins that possess different chromatin-modifying activities.
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Affiliation(s)
- K S Egorova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
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31
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Tooley CES, Petkowski JJ, Muratore-Schroeder TL, Balsbaugh JL, Shabanowitz J, Sabat M, Minor W, Hunt DF, Macara IG. NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein. Nature 2010; 466:1125-8. [PMID: 20668449 PMCID: PMC2939154 DOI: 10.1038/nature09343] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 08/26/2010] [Accepted: 07/08/2010] [Indexed: 11/16/2022]
Abstract
The post-translational methylation of α-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L331–2, but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be α-N-methylated3–10. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of α-N-methylation has been identified3, 11. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects3, 11, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating they may be targets of the same, unknown enzyme3,12. The initiating Met is cleaved, and the exposed α-amino group is mono-, di-, or trimethylated. Here we report the discovery of the first α-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET/TAF-I/PHAPII and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants3, demonstrating the importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation.
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Affiliation(s)
- Christine E Schaner Tooley
- Department of Microbiology, Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.
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32
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Webb KJ, Lipson RS, Al-Hadid Q, Whitelegge JP, Clarke SG. Identification of protein N-terminal methyltransferases in yeast and humans. Biochemistry 2010; 49:5225-35. [PMID: 20481588 DOI: 10.1021/bi100428x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein modification by methylation is important in cellular function. We show here that the Saccharomyces cerevisiae YBR261C/TAE1 gene encodes an N-terminal protein methyltransferase catalyzing the modification of two ribosomal protein substrates, Rpl12ab and Rps25a/Rps25b. The YBR261C/Tae1 protein is conserved across eukaryotes; all of these proteins share sequence similarity with known seven beta-strand class I methyltransferases. Wild-type yeast cytosol and mouse heart cytosol catalyze the methylation of a synthetic peptide (PPKQQLSKY) that contains the first eight amino acids of the processed N-terminus of Rps25a/Rps25b. However, no methylation of this peptide is seen in yeast cytosol from a DeltaYBR261C/tae1 deletion strain. Yeast YBR261C/TAE1 and the human orthologue METTL11A genes were expressed as fusion proteins in Escherichia coli and were shown to be capable of stoichiometrically dimethylating the N-terminus of the synthetic peptide. Furthermore, the YBR261C/Tae1 and METTL11A recombinant proteins methylate variants of the synthetic peptide containing N-terminal alanine and serine residues. However, methyltransferase activity is largely abolished when the proline residue in position 2 or the lysine residue in position 3 is substituted. Thus, the methyltransferases described here specifically recognize the N-terminal X-Pro-Lys sequence motif, and we suggest designating the yeast enzyme Ntm1 and the human enzyme NTMT1. These enzymes may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and human proteins also share the recognition motif and may be similarly modified. We conclude that protein X-Pro-Lys N-terminal methylation reactions catalyzed by the enzymes described here may be widespread in nature.
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Affiliation(s)
- Kristofor J Webb
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA
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Shirai A, Sadaie M, Shinmyozu K, Nakayama JI. Methylation of ribosomal protein L42 regulates ribosomal function and stress-adapted cell growth. J Biol Chem 2010; 285:22448-60. [PMID: 20444689 DOI: 10.1074/jbc.m110.132274] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine methylation is one of the most common protein modifications. Although lysine methylation of histones has been extensively studied and linked to gene regulation, that of non-histone proteins remains incompletely understood. Here, we show a novel regulatory role of ribosomal protein methylation. Using an in vitro methyltransferase assay, we found that Schizosaccharomyces pombe Set13, a SET domain protein encoded by SPAC688.14, specifically methylates lysine 55 of ribosomal protein L42 (Rpl42). Mass spectrometric analysis revealed that endogenous Rpl42 is monomethylated at lysine 55 in wild-type S. pombe cells and that the methylation is lost in Delta set13 mutant cells. Delta set13 and Rpl42 methylation-deficient mutant S. pombe cells showed higher cycloheximide sensitivity and defects in stress-responsive growth control compared with wild type. Genetic analyses suggested that the abnormal growth phenotype was distinct from the conserved stress-responsive pathway that modulates translation initiation. Furthermore, the Rpl42 methylation-deficient mutant cells showed a reduced ability to survive after entering stationary phase. These results suggest that Rpl42 methylation plays direct roles in ribosomal function and cell proliferation control independently of the general stress-response pathway.
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Affiliation(s)
- Atsuko Shirai
- Laboratory for Chromatin Dynamics, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
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34
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Pang CNI, Gasteiger E, Wilkins MR. Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. BMC Genomics 2010; 11:92. [PMID: 20137074 PMCID: PMC2830191 DOI: 10.1186/1471-2164-11-92] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 02/05/2010] [Indexed: 02/07/2023] Open
Abstract
Background The methylation of eukaryotic proteins has been proposed to be widespread, but this has not been conclusively shown to date. In this study, we examined 36,854 previously generated peptide mass spectra from 2,607 Saccharomyces cerevisiae proteins for the presence of arginine and lysine methylation. This was done using the FindMod tool and 5 filters that took advantage of the high number of replicate analysis per protein and the presence of overlapping peptides. Results A total of 83 high-confidence lysine and arginine methylation sites were found in 66 proteins. Motif analysis revealed many methylated sites were associated with MK, RGG/RXG/RGX or WXXXR motifs. Functionally, methylated proteins were significantly enriched for protein translation, ribosomal biogenesis and assembly and organellar organisation and were predominantly found in the cytoplasm and ribosome. Intriguingly, methylated proteins were seen to have significantly longer half-life than proteins for which no methylation was found. Some 43% of methylated lysine sites were predicted to be amenable to ubiquitination, suggesting methyl-lysine might block the action of ubiquitin ligase. Conclusions This study suggests protein methylation to be quite widespread, albeit associated with specific functions. Large-scale tandem mass spectroscopy analyses will help to further confirm the modifications reported here.
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Affiliation(s)
- Chi Nam Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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35
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Perreault A, Gascon S, D'Amours A, Aletta JM, Bachand F. A methyltransferase-independent function for Rmt3 in ribosomal subunit homeostasis. J Biol Chem 2009; 284:15026-37. [PMID: 19359250 DOI: 10.1074/jbc.m109.004812] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Schizosaccharomyces pombe Rmt3 is a member of the protein-arginine methyltransferase (PRMT) family and is the homolog of human PRMT3. We previously characterized Rmt3 as a ribosomal protein methyltransferase based on the identification of the 40 S Rps2 (ribosomal protein S2) as a substrate of Rmt3. RMT3-null cells produce nonmethylated Rps2 and show mis-regulation of the 40 S/60 S ribosomal subunit ratio due to a small subunit deficit. For this study, we have generated a series of RMT3 alleles that express various amino acid substitutions to characterize the functional domains of Rmt3 in Rps2 binding, Rps2 arginine methylation, and small ribosomal subunit production. Notably, catalytically inactive versions of Rmt3 restored the ribosomal subunit imbalance detected in RMT3-null cells. Consistent with a methyltransferase-independent function for Rmt3 in small ribosomal subunit production, the expression of an Rps2 variant in which the identified methylarginine residues were substituted with lysines showed normal levels of 40 S subunit. Importantly, substitutions within the zinc finger domain of Rmt3 that abolished Rps2 binding did not rescue the 40 S ribosomal subunit deficit of RMT3-null cells. Our findings suggest that the Rmt3-Rps2 interaction, rather than Rps2 methylation, is important for the function of Rmt3 in the regulation of small ribosomal subunit production.
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Affiliation(s)
- Audrey Perreault
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Québec J1H 5N4, Canada
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36
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Webb KJ, Laganowsky A, Whitelegge JP, Clarke SG. Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab. J Biol Chem 2008; 283:35561-8. [PMID: 18957409 DOI: 10.1074/jbc.m806006200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We show that the Saccharomyces cerevisiae ribosomal protein Rpl42ab (the identical product of the RPL42A and RPL42B genes) is monomethylated at Lys-40 and Lys-55. The methylation of Lys-40 is dependent upon the Ybr030w gene product; the methylation of Lys-55 is dependent upon the Set7 gene product. Ybr030w and SET7 genes both encode SET domain containing proteins homologous to known protein lysine methyltransferases, suggesting that their products are the specific enzymes responsible for the monomethylation of the two sites in Rpl42ab. We thus designate Ybr030w as Rkm3 and Set7 as Rkm4. Yeast strains with deletions in both the Ybr030w and SET7 genes produce unmethylated Rpl42ab. A slow growth phenotype was seen for the SET7 deletion strain and the double knock-out when grown in low concentrations of the eukaryotic protein synthesis inhibitor, cycloheximide. These results suggest that modification of Rpl42ab at Lys-55 can fine-tune its structure to avoid inhibition. An intact mass fragmentation approach ("top down mass spectrometry") was used to quantitate the extent of methylation of Rpl42ab. In wild-type strains, it was found that 78% was monomethylated at both Lys-40 and Lys-55 and that 22% was a mixture of species with either Lys-40 or Lys-55 monomethylated. The top down approach was also used to reevaluate the methylation sites of Rpl12ab. We found that the yeast Rpl12ab protein is dimethylated at the N-terminal proline residue, trimethylated at Lys-3 by Rkm2, and monomethylated at Arg-66.
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Affiliation(s)
- Kristofor J Webb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
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37
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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