1
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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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2
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Zhang H, Kuang Z, Xue L, Yue J, Khan MH, Zhu Z, Niu L. Structural Basis for Peptide Binding of α-N Terminal Methyltransferase from Saccharomyces cerevisiae. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521070257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Pokrovsky D, Forné I, Straub T, Imhof A, Rupp RAW. A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis. PLoS Biol 2021; 19:e3001377. [PMID: 34491983 PMCID: PMC8535184 DOI: 10.1371/journal.pbio.3001377] [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: 08/21/2020] [Revised: 10/22/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Forming an embryo from a zygote poses an apparent conflict for epigenetic regulation. On the one hand, the de novo induction of cell fate identities requires the establishment and subsequent maintenance of epigenetic information to harness developmental gene expression. On the other hand, the embryo depends on cell proliferation, and every round of DNA replication dilutes preexisting histone modifications by incorporation of new unmodified histones into chromatin. Here, we investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis. We systemically inhibited cell proliferation during the G1/S transition in gastrula embryos and followed their development until the tadpole stage. Comparing wild-type and cell cycle-arrested embryos, we show that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation. In parallel, we quantified by mass spectrometry the abundance of a large set of histone modification states, which reflects the developmental maturation of the embryonic epigenome. The arrested embryos developed abnormal stage-specific histone modification profiles (HMPs), in which transcriptionally repressive histone marks were overrepresented. Embryos released from the cell cycle block during neurulation reverted toward normality on morphological, molecular, and epigenetic levels. These results suggest that the cell cycle block by HUA alters stage-specific HMPs. We propose that this influence is strong enough to control developmental decisions, specifically in cell populations that switch between resting and proliferating states such as stem cells.
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Affiliation(s)
- Daniil Pokrovsky
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ignasi Forné
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Straub
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Axel Imhof
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ralph A. W. Rupp
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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4
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Rommelfanger S, Zhou M, Shaghasi H, Tzeng SC, Evans BS, Paša-Tolić L, Umen JG, Pesavento JJ. An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1671-1688. [PMID: 34165968 PMCID: PMC9236284 DOI: 10.1021/jasms.1c00029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/01/2023]
Abstract
We present an updated analysis of the linker and core histone proteins and their proteoforms in the green microalga Chlamydomonas reinhardtii by top-down mass spectrometry (TDMS). The combination of high-resolution liquid chromatographic separation, robust fragmentation, high mass spectral resolution, the application of a custom search algorithm, and extensive manual analysis enabled the characterization of 86 proteoforms across all four core histones H2A, H2B, H3, and H4 and the linker histone H1. All canonical H2A paralogs, which vary in their C-termini, were identified, along with the previously unreported noncanonical variant H2A.Z that had high levels of acetylation and C-terminal truncations. Similarly, a majority of the canonical H2B paralogs were identified, along with a smaller noncanonical variant, H2B.v1, that was highly acetylated. Histone H4 exhibited a novel acetylation profile that differs significantly from that found in other organisms. A majority of H3 was monomethylated at K4 with low levels of co-occuring acetylation, while a small fraction of H3 was trimethylated at K4 with high levels of co-occuring acetylation.
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Affiliation(s)
- Sarah
R. Rommelfanger
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
- Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Henna Shaghasi
- Saint
Mary’s College of California, Moraga, California 94575, United States
| | - Shin-Cheng Tzeng
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
| | - Bradley S. Evans
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
| | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - James G. Umen
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
- Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - James J. Pesavento
- Saint
Mary’s College of California, Moraga, California 94575, United States
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5
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Past, present, and perspectives of protein N-terminal methylation. Curr Opin Chem Biol 2021; 63:115-122. [PMID: 33839647 DOI: 10.1016/j.cbpa.2021.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 01/16/2023]
Abstract
The posttranslational methylation of the α-N-terminal amino group of proteins was first documented over 40 years ago, but the functional significance of this modification has been underexplored relative to lysine and arginine methylation. Increasing reports implicates α-N-terminal methylation as a widespread and critical regulator of mitosis, chromatin interactions, DNA repair, and translation fidelity. Here, we summarize advances in the current understanding of protein α-N-terminal methylation biological functions and mechanisms across eukaryotic organisms. Also, we describe the recent literature on substrate recognition and the discovery of potent and selective inhibitors for protein N-terminal methyltransferases. Finally, we summarize the emergent crosstalk between α-N-terminal methylation and other N-terminal modifications.
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6
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Schuh L, Loos C, Pokrovsky D, Imhof A, Rupp RAW, Marr C. H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos. Cell Syst 2020; 11:653-662.e8. [PMID: 33296683 DOI: 10.1016/j.cels.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/05/2020] [Accepted: 11/11/2020] [Indexed: 11/26/2022]
Abstract
DNA replication during cell division leads to dilution of histone modifications and can thus affect chromatin-mediated gene regulation, raising the question of how the cell-cycle shapes the histone modification landscape, particularly during embryogenesis. We tackled this problem by manipulating the cell cycle during early Xenopus laevis embryogenesis and analyzing in vivo histone H4K20 methylation kinetics. The global distribution of un-, mono-, di-, and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle-arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific biological methylation rate constants were required to explain the measured H4K20 methylation state kinetics. While demethylation is essential for regulating H4K20 methylation kinetics in non-cycling cells, demethylation is very likely dispensable in rapidly dividing cells of early embryos, suggesting that cell-cycle-mediated dilution of H4K20 methylation is an essential regulatory component for shaping its epigenetic landscape during early development. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Lea Schuh
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniil Pokrovsky
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Axel Imhof
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Ralph A W Rupp
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany.
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7
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Demetriadou C, Koufaris C, Kirmizis A. Histone N-alpha terminal modifications: genome regulation at the tip of the tail. Epigenetics Chromatin 2020; 13:29. [PMID: 32680559 PMCID: PMC7367250 DOI: 10.1186/s13072-020-00352-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/09/2020] [Indexed: 01/07/2023] Open
Abstract
Histone proteins are decorated with numerous post-(PTMs) or co-(CTMs) translational modifications mainly on their unstructured tails, but also on their globular domain. For many decades research on histone modifications has been focused almost solely on the biological role of modifications occurring at the side-chain of internal amino acid residues. In contrast, modifications on the terminal N-alpha amino group of histones-despite being highly abundant and evolutionarily conserved-have been largely overlooked. This oversight has been due to the fact that these marks were being considered inert until recently, serving no regulatory functions. However, during the past few years accumulating evidence has drawn attention towards the importance of chemical marks added at the very N-terminal tip of histones and unveiled their role in key biological processes including aging and carcinogenesis. Further elucidation of the molecular mechanisms through which these modifications are regulated and by which they act to influence chromatin dynamics and DNA-based processes like transcription is expected to enlighten our understanding of their emerging role in controlling cellular physiology and contribution to human disease. In this review, we clarify the difference between N-alpha terminal (Nt) and internal (In) histone modifications; provide an overview of the different types of known histone Nt-marks and the associated histone N-terminal transferases (NTTs); and explore how they function to shape gene expression, chromatin architecture and cellular phenotypes.
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Affiliation(s)
- Christina Demetriadou
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Costas Koufaris
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Antonis Kirmizis
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus.
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8
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Bonnet J, Lindeboom RGH, Pokrovsky D, Stricker G, Çelik MH, Rupp RAW, Gagneur J, Vermeulen M, Imhof A, Müller J. Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation. Dev Cell 2019; 51:632-644.e6. [PMID: 31630981 DOI: 10.1016/j.devcel.2019.09.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/09/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Gene transcription in eukaryotes is regulated through dynamic interactions of a variety of different proteins with DNA in the context of chromatin. Here, we used mass spectrometry for absolute quantification of the nuclear proteome and methyl marks on selected lysine residues in histone H3 during two stages of Drosophila embryogenesis. These analyses provide comprehensive information about the absolute copy number of several thousand proteins and reveal unexpected relationships between the abundance of histone-modifying and -binding proteins and the chromatin landscape that they generate and interact with. For some histone modifications, the levels in Drosophila embryos are substantially different from those previously reported in tissue culture cells. Genome-wide profiling of H3K27 methylation during developmental progression and in animals with reduced PRC2 levels illustrates how mass spectrometry can be used for quantitatively describing and comparing chromatin states. Together, these data provide a foundation toward a quantitative understanding of gene regulation in Drosophila.
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Affiliation(s)
- Jacques Bonnet
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rik G H Lindeboom
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Department of Molecular Biology, Radboud University, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Daniil Pokrovsky
- Institute for Molecular Biology, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany; Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Georg Stricker
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Muhammed Hasan Çelik
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Ralph A W Rupp
- Institute for Molecular Biology, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Department of Molecular Biology, Radboud University, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands.
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany.
| | - Jürg Müller
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.
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9
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Abstract
Protein α‐N‐terminal methylation is catalyzed by protein N‐terminal methyltransferases. The prevalent occurrence of this methylation in ribosomes, myosin, and histones implies its function in protein–protein interactions. Although its full spectrum of function has not yet been outlined, recent discoveries have revealed the emerging roles of α‐N‐terminal methylation in protein–chromatin interactions, DNA damage repair, and chromosome segregation. Herein, an overview of the discovery of protein N‐terminal methyltransferases and functions of α‐N‐terminal methylation is presented. In addition, substrate recognition, mechanisms, and inhibition of N‐terminal methyltransferases are reviewed. Opportunities and gaps in protein α‐N‐terminal methylation are also discussed.
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Affiliation(s)
- Rong Huang
- Department of Medicinal Chemistry and Molecular PharmacologyCenter for Cancer Research, Institute for Drug DiscoveryPurdue University West Lafayette IN 47907 USA
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10
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Dong C, Dong G, Li L, Zhu L, Tempel W, Liu Y, Huang R, Min J. An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2. Commun Biol 2018; 1:183. [PMID: 30417120 PMCID: PMC6214909 DOI: 10.1038/s42003-018-0196-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/15/2018] [Indexed: 01/11/2023] Open
Abstract
α-N-terminal methylation of proteins is an important post-translational modification that is catalyzed by two different N-terminal methyltransferases, namely NTMT1 and NTMT2. Previous studies have suggested that NTMT1 is a tri-methyltransferase, whereas NTMT2 is a mono-methyltransferase. Here, we report the first crystal structures, to our knowledge, of NTMT2 in binary complex with S-adenosyl-L-methionine as well as in ternary complex with S-adenosyl-L-homocysteine and a substrate peptide. Our structural observations combined with biochemical studies reveal that NTMT2 is also able to di-/tri-methylate the GPKRIA peptide and di-methylate the PPKRIA peptide, otherwise it is predominantly a mono-methyltransferase. The residue N89 of NTMT2 serves as a gatekeeper residue that regulates the binding of unmethylated versus monomethylated substrate peptide. Structural comparison of NTMT1 and NTMT2 prompts us to design a N89G mutant of NTMT2 that can profoundly alter its catalytic activities and product specificities. Cheng Dong et al. resolve the crystal structure of NTMT2, presenting the molecular basis for substrate recognition. Using structural and biochemical studies, they identified a specific residue within NTMT2 that controls its binding affinity to unmethylated or monomethylated substrates.
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Affiliation(s)
- Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Guangping Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Licheng Zhu
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada.,School of Life Sciences, Jinggangshan University, 343009, Ji'an, Jiangxi, China
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA.
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada. .,Department of Physiology, University of Toronto, Toronto, M5S 1A8, ON, Canada.
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11
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Wu R, Yue Y, Zheng X, Li H. Molecular basis for histone N-terminal methylation by NRMT1. Genes Dev 2015; 29:2337-42. [PMID: 26543159 PMCID: PMC4691888 DOI: 10.1101/gad.270926.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/09/2015] [Indexed: 02/05/2023]
Abstract
NRMT1 is an N-terminal methyltransferase that methylates histone CENP-A as well as nonhistone substrates. Wu et al. report the crystal structure of human NRMT1 bound to CENP-A peptide at 1.3 Å. NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases. NRMT1 is an N-terminal methyltransferase that methylates histone CENP-A as well as nonhistone substrates. Here, we report the crystal structure of human NRMT1 bound to CENP-A peptide at 1.3 Å. NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases. Key substrate recognition and catalytic residues were identified by mutagenesis studies. Histone peptide profiling revealed that human NRMT1 is highly selective to human CENP-A and fruit fly H2B, which share a common “Xaa-Pro–Lys/Arg” motif. These results, along with a 1.5 Å costructure of human NRMT1 bound to the fruit fly H2B peptide, underscore the importance of the NRMT1 recognition motif.
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Affiliation(s)
- Ruoxi Wu
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuan Yue
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangdong Zheng
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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12
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Dong C, Mao Y, Tempel W, Qin S, Li L, Loppnau P, Huang R, Min J. Structural basis for substrate recognition by the human N-terminal methyltransferase 1. Genes Dev 2015; 29:2343-8. [PMID: 26543161 PMCID: PMC4691889 DOI: 10.1101/gad.270611.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/14/2015] [Indexed: 01/17/2023]
Abstract
α-N-terminal methylation represents a highly conserved and prevalent post-translational modification, yet its biological function has remained largely speculative. The recent discovery of α-N-terminal methyltransferase 1 (NTMT1) and its physiological substrates propels the elucidation of a general role of α-N-terminal methylation in mediating DNA-binding ability of the modified proteins. The phenotypes, observed from both NTMT1 knockdown in breast cancer cell lines and knockout mouse models, suggest the potential involvement of α-N-terminal methylation in DNA damage response and cancer development. In this study, we report the first crystal structures of human NTMT1 in complex with cofactor S-adenosyl-L-homocysteine (SAH) and six substrate peptides, respectively, and reveal that NTMT1 contains two characteristic structural elements (a β hairpin and an N-terminal extension) that contribute to its substrate specificity. Our complex structures, coupled with mutagenesis, binding, and enzymatic studies, also present the key elements involved in locking the consensus substrate motif XPK (X indicates any residue type other than D/E) into the catalytic pocket for α-N-terminal methylation and explain why NTMT1 prefers an XPK sequence motif. We propose a catalytic mechanism for α-N-terminal methylation. Overall, this study gives us the first glimpse of the molecular mechanism of α-N-terminal methylation and potentially contributes to the advent of therapeutic agents for human diseases associated with deregulated α-N-terminal methylation.
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Affiliation(s)
- Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Yunfei Mao
- Department of Medicinal Chemistry, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA; The Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Rong Huang
- Department of Medicinal Chemistry, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA; The Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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13
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Zhang G, Richardson SL, Mao Y, Huang R. Design, synthesis, and kinetic analysis of potent protein N-terminal methyltransferase 1 inhibitors. Org Biomol Chem 2015; 13:4149-54. [PMID: 25712161 PMCID: PMC4857722 DOI: 10.1039/c5ob00120j] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The protein N-terminal methyltransferase 1 (NTMT1) methylates the α-N-terminal amines of proteins. NTMT1 is upregulated in a variety of cancers and knockdown of NTMT1 results in cell mitotic defects. Therefore, NTMT1 inhibitors could be potential anticancer therapeutics. This study describes the design and synthesis of the first inhibitor targeting NTMT1. A novel bisubstrate analogue (NAM-TZ-SPKRIA) was shown to be a potent inhibitor (Ki = 0.20 μM) for NTMT1 and was selective versus protein lysine methyltransferase G9a and arginine methyltransferase 1. NAM-TZ-SPKRIA was found to exhibit a competitive inhibition pattern for both substrates, and mass spectrometry experiments revealed that the inhibitor substantially suppressed the methylation progression. Our results demonstrate the feasibility of using a triazole group to link an S-adenosyl-L-methionine analog with a peptide substrate to construct bisubstrate analogues as NTMT1 potent and selective inhibitors. This study lays a foundation to further discover small molecule NTMT1 inhibitors to interrogate its biological functions, and suggests a general strategy for the development of selective protein methyltransferase inhibitors.
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Affiliation(s)
- Gang Zhang
- Department of Medicinal Chemistry, and the Institute of Structural Biology & Drug Discovery, Virginia Commonwealth University, Richmond, VA, USA.
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14
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Richardson SL, Mao Y, Zhang G, Hanjra P, Peterson DL, Huang R. Kinetic mechanism of protein N-terminal methyltransferase 1. J Biol Chem 2015; 290:11601-10. [PMID: 25771539 DOI: 10.1074/jbc.m114.626846] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 01/10/2023] Open
Abstract
The protein N-terminal methyltransferase 1 (NTMT1) catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine to the protein α-amine, resulting in formation of S-adenosyl-l-homocysteine and α-N-methylated proteins. NTMT1 is an interesting potential anticancer target because it is overexpressed in gastrointestinal cancers and plays an important role in cell mitosis. To gain insight into the biochemical mechanism of NTMT1, we have characterized the kinetic mechanism of recombinant NTMT1 using a fluorescence assay and mass spectrometry. The results of initial velocity, product, and dead-end inhibition studies indicate that methylation by NTMT1 proceeds via a random sequential Bi Bi mechanism. In addition, our processivity studies demonstrate that NTMT1 proceeds via a distributive mechanism for multiple methylations. Together, our studies provide new knowledge about the kinetic mechanism of NTMT1 and lay the foundation for the development of mechanism-based inhibitors.
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Affiliation(s)
- Stacie L Richardson
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Yunfei Mao
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Gang Zhang
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Pahul Hanjra
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Darrell L Peterson
- the Institute for Structural Biology and Drug Discovery, and the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Rong Huang
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
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15
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Tooley JG, Schaner Tooley CE. New roles for old modifications: emerging roles of N-terminal post-translational modifications in development and disease. Protein Sci 2014; 23:1641-9. [PMID: 25209108 DOI: 10.1002/pro.2547] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/08/2014] [Indexed: 01/07/2023]
Abstract
The importance of internal post-translational modification (PTM) in protein signaling and function has long been known and appreciated. However, the significance of the same PTMs on the alpha amino group of N-terminal amino acids has been comparatively understudied. Historically considered static regulators of protein stability, additional functional roles for N-terminal PTMs are now beginning to be elucidated. New findings show that N-terminal methylation, along with N-terminal acetylation, is an important regulatory modification with significant roles in development and disease progression. There are also emerging studies on the enzymology and functional roles of N-terminal ubiquitylation and N-terminal propionylation. Here, will discuss the recent advances in the functional studies of N-terminal PTMs, recount the new N-terminal PTMs being identified, and briefly examine the possibility of dynamic N-terminal PTM exchange.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry and Molecular Biology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky
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16
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Lacoste N, Woolfe A, Tachiwana H, Garea AV, Barth T, Cantaloube S, Kurumizaka H, Imhof A, Almouzni G. Mislocalization of the centromeric histone variant CenH3/CENP-A in human cells depends on the chaperone DAXX. Mol Cell 2014; 53:631-44. [PMID: 24530302 DOI: 10.1016/j.molcel.2014.01.018] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 10/02/2013] [Accepted: 01/07/2014] [Indexed: 01/17/2023]
Abstract
Centromeres are essential for ensuring proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover involving a heterotypic tetramer containing CenH3-H4 with H3.3-H4. Ectopic localization of this particle depends on the H3.3 chaperone DAXX rather than the dedicated CenH3 chaperone HJURP. This aberrant nucleosome occludes CTCF binding and has a minor effect on gene expression. Cells overexpressing CenH3 are more tolerant of DNA damage. Both the survival advantage and CTCF occlusion in these cells are dependent on DAXX. Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics and suggests a possible mechanism for cell resistance to anticancer treatments.
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Affiliation(s)
- Nicolas Lacoste
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Adam Woolfe
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Hiroaki Tachiwana
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Ana Villar Garea
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Teresa Barth
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Axel Imhof
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France.
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17
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Dillinger S, Garea AV, Deutzmann R, Németh A. Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry. Methods Mol Biol 2014; 1094:277-93. [PMID: 24162996 DOI: 10.1007/978-1-62703-706-8_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin is unevenly distributed within the eukaryote nucleus and it contributes to the formation of morphologically and functionally distinct substructures, called chromatin domains and nuclear bodies. Here we describe an approach to assess specific chromatin features, the histone posttranslational modifications (PTMs), of the largest nuclear sub-compartment, the nucleolus. In this chapter, methods for the isolation of nucleolus-associated chromatin from native or formaldehyde-fixed cells and the effect of experimental procedures on the outcome of mass spectrometry analysis of histone PTMs are compared.
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Affiliation(s)
- Stefan Dillinger
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
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18
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Kimura Y, Kurata Y, Ishikawa A, Okayama A, Kamita M, Hirano H. N-Terminal methylation of proteasome subunit Rpt1 in yeast. Proteomics 2013; 13:3167-74. [DOI: 10.1002/pmic.201300207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/21/2013] [Accepted: 08/28/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Yayoi Kimura
- Graduate School of Medical Life Science and Advanced Medical Research Center; Yokohama City University; Yokohama Japan
| | - Yoichi Kurata
- Graduate School of Medical Life Science and Advanced Medical Research Center; Yokohama City University; Yokohama Japan
| | - Akiyo Ishikawa
- Graduate School of Medical Life Science and Advanced Medical Research Center; Yokohama City University; Yokohama Japan
| | - Akiko Okayama
- Graduate School of Medical Life Science and Advanced Medical Research Center; Yokohama City University; Yokohama Japan
| | - Masahiro Kamita
- Graduate School of Medical Life Science and Advanced Medical Research Center; Yokohama City University; Yokohama Japan
| | - Hisashi Hirano
- Graduate School of Medical Life Science and Advanced Medical Research Center; Yokohama City University; Yokohama Japan
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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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Cross-talk among epigenetic modifications: lessons from histone arginine methylation. Biochem Soc Trans 2013; 41:751-9. [DOI: 10.1042/bst20130003] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications, including those occurring on DNA and on histone proteins, control gene expression by establishing and maintaining different chromatin states. In recent years, it has become apparent that epigenetic modifications do not function alone, but work together in various combinations, and cross-regulate each other in a manner that diversifies their functional states. Arginine methylation is one of the numerous PTMs (post-translational modifications) occurring on histones, catalysed by a family of PRMTs (protein arginine methyltransferases). This modification is involved in the regulation of the epigenome largely by controlling the recruitment of effector molecules to chromatin. Histone arginine methylation associates with both active and repressed chromatin states depending on the residue involved and the configuration of the deposited methyl groups. The present review focuses on the increasing number of cross-talks between histone arginine methylation and other epigenetic modifications, and describe how these cross-talks influence factor binding to regulate transcription. Furthermore, we present models of general cross-talk mechanisms that emerge from the examples of histone arginine methylation and allude to various techniques that help decipher the interplay among epigenetic modifications.
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21
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Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. Int J Mol Sci 2013; 14:5402-31. [PMID: 23466885 PMCID: PMC3634404 DOI: 10.3390/ijms14035402] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/24/2013] [Accepted: 02/20/2013] [Indexed: 12/22/2022] Open
Abstract
Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific "chromatin landscape", with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from "Bottom Up" to "Top Down" analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.
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22
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Abstract
Epigenetics is a major field of biomedical research, and epigenetic drug discovery shows great promise for new drugs. The first epigenetic inhibitors are already approved for human treatment. Here, we review a number of case studies that cover different aspects of epigenetic drug discovery spanning from sequencing of epigenetic modifications, assays development over screening to medicinal chemistry, in vivo testing and clinical application.
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23
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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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