101
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Zhang H, Amick J, Chakravarti R, Santarriaga S, Schlanger S, McGlone C, Dare M, Nix JC, Scaglione KM, Stuehr DJ, Misra S, Page RC. A bipartite interaction between Hsp70 and CHIP regulates ubiquitination of chaperoned client proteins. Structure 2015; 23:472-482. [PMID: 25684577 DOI: 10.1016/j.str.2015.01.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/24/2014] [Accepted: 01/05/2015] [Indexed: 11/16/2022]
Abstract
The ubiquitin ligase CHIP plays an important role in cytosolic protein quality control by ubiquitinating proteins chaperoned by Hsp70/Hsc70 and Hsp90, thereby targeting such substrate proteins for degradation. We present a 2.91 Å resolution structure of the tetratricopeptide repeat (TPR) domain of CHIP in complex with the α-helical lid subdomain and unstructured tail of Hsc70. Surprisingly, the CHIP-TPR interacts with determinants within both the Hsc70-lid subdomain and the C-terminal PTIEEVD motif of the tail, exhibiting an atypical mode of interaction between chaperones and TPR domains. We demonstrate that the interaction between CHIP and the Hsc70-lid subdomain is required for proper ubiquitination of Hsp70/Hsc70 or Hsp70/Hsc70-bound substrate proteins. Posttranslational modifications of the Hsc70 lid and tail disrupt key contacts with the CHIP-TPR and may regulate CHIP-mediated ubiquitination. Our study shows how CHIP docks onto Hsp70/Hsc70 and defines a bipartite mode of interaction between TPR domains and their binding partners.
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Affiliation(s)
- Huaqun Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Joseph Amick
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ritu Chakravarti
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Simon Schlanger
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cameron McGlone
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Michelle Dare
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jay C Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - K Matthew Scaglione
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Dennis J Stuehr
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurav Misra
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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102
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Małecki J, Ho AYY, Moen A, Dahl HA, Falnes PØ. Human METTL20 is a mitochondrial lysine methyltransferase that targets the β subunit of electron transfer flavoprotein (ETFβ) and modulates its activity. J Biol Chem 2014; 290:423-34. [PMID: 25416781 DOI: 10.1074/jbc.m114.614115] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Proteins are frequently modified by post-translational methylation of lysine residues, catalyzed by S-adenosylmethionine-dependent lysine methyltransferases (KMTs). Lysine methylation of histone proteins has been extensively studied, but it has recently become evident that methylation of non-histone proteins is also abundant and important. The human methyltransferase METTL20 belongs to a group of 10 established and putative human KMTs. We here found METTL20 to be associated with mitochondria and determined that recombinant METTL20 methylated a single protein in extracts from human cells. Using an methyltransferase activity-based purification scheme, we identified the β-subunit of the mitochondrially localized electron transfer flavoprotein (ETFβ) as the substrate of METTL20. Furthermore, METTL20 was found to specifically methylate two adjacent lysine residues, Lys(200) and Lys(203), in ETFβ both in vitro and in cells. Interestingly, the residues methylated by METTL20 partially overlap with the so-called "recognition loop" in ETFβ, which has been shown to mediate its interaction with various dehydrogenases. Accordingly, we found that METTL20-mediated methylation of ETFβ in vitro reduced its ability to receive electrons from the medium chain acyl-CoA dehydrogenase and the glutaryl-CoA dehydrogenase. In conclusion, the present study establishes METTL20 as the first human KMT localized to mitochondria and suggests that it may regulate cellular metabolism through modulating the interaction between its substrate ETFβ and dehydrogenases. Based on the previous naming of similar enzymes, we suggest the renaming of human METTL20 to ETFβ-KMT.
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Affiliation(s)
- Jędrzej Małecki
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Angela Y Y Ho
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Anders Moen
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Helge-André Dahl
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Pål Ø Falnes
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
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103
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Taldone T, Ochiana SO, Patel PD, Chiosis G. Selective targeting of the stress chaperome as a therapeutic strategy. Trends Pharmacol Sci 2014; 35:592-603. [PMID: 25262919 DOI: 10.1016/j.tips.2014.09.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/28/2014] [Accepted: 09/02/2014] [Indexed: 12/11/2022]
Abstract
Normal cellular function is maintained by coordinated proteome machinery that performs a vast array of activities. Helping the proteome in such roles is the chaperome, a network of molecular chaperones and folding enzymes. The stressed cell contains, at any time, a complex mixture of chaperome complexes; a majority performs 'housekeeping functions' similarly to non-stressed, normal cells, but a finely-tuned fraction buffers the proteome altered by chronic stress. The stress chaperome is epigenetically distinct from its normal, housekeeping counterpart, providing a basis for its selective targeting by small molecules. We discuss here the development of chaperome inhibitors, and how agents targeting chaperome members in stressed cells are in fact being directed towards chaperome complexes, and their effect is therefore determined by their ability to sample and engage such complexes. A new approach is needed to target and implement chaperome modulators in the investigation of diseases, and we propose that the classical thinking in drug discovery needs adjustment when developing chaperome-targeting drugs.
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Affiliation(s)
- Tony Taldone
- Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stefan O Ochiana
- Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pallav D Patel
- Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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104
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Davydova E, Ho AYY, Malecki J, Moen A, Enserink JM, Jakobsson ME, Loenarz C, Falnes PØ. Identification and characterization of a novel evolutionarily conserved lysine-specific methyltransferase targeting eukaryotic translation elongation factor 2 (eEF2). J Biol Chem 2014; 289:30499-30510. [PMID: 25231979 DOI: 10.1074/jbc.m114.601658] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The components of the cellular protein translation machinery, such as ribosomal proteins and translation factors, are subject to numerous post-translational modifications. In particular, this group of proteins is frequently methylated. However, for the majority of these methylations, the responsible methyltransferases (MTases) remain unknown. The human FAM86A (family with sequence similarity 86) protein belongs to a recently identified family of protein MTases, and we here show that FAM86A catalyzes the trimethylation of eukaryotic elongation factor 2 (eEF2) on Lys-525. Moreover, we demonstrate that the Saccharomyces cerevisiae MTase Yjr129c, which displays sequence homology to FAM86A, is a functional FAM86A orthologue, modifying the corresponding residue (Lys-509) in yeast eEF2, both in vitro and in vivo. Finally, Yjr129c-deficient yeast cells displayed phenotypes related to eEF2 function (i.e. increased frameshifting during protein translation and hypersensitivity toward the eEF2-specific drug sordarin). In summary, the present study establishes the function of the previously uncharacterized MTases FAM86A and Yjr129c, demonstrating that these enzymes introduce a functionally important lysine methylation in eEF2. Based on the previous naming of similar enzymes, we have redubbed FAM86A and Yjr129c as eEF2-KMT and Efm3, respectively.
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Affiliation(s)
- Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jedrzej Malecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jorrit M Enserink
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0027 Oslo, Norway, and
| | - Magnus E Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Christoph Loenarz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway,.
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105
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Shimazu T, Barjau J, Sohtome Y, Sodeoka M, Shinkai Y. Selenium-based S-adenosylmethionine analog reveals the mammalian seven-beta-strand methyltransferase METTL10 to be an EF1A1 lysine methyltransferase. PLoS One 2014; 9:e105394. [PMID: 25144183 PMCID: PMC4140779 DOI: 10.1371/journal.pone.0105394] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/21/2014] [Indexed: 12/17/2022] Open
Abstract
Lysine methylation has been extensively studied in histones, where it has been shown to provide specific epigenetic marks for the regulation of gene expression; however, the molecular mechanism and physiological function of lysine methylation in proteins other than histones remains to be fully addressed. To better understand the substrate diversity of lysine methylation, S-adenosylmethionine (SAM) derivatives with alkyne-moieties have been synthesized. A selenium-based SAM analog, propargylic Se-adenosyl-l-selenomethionine (ProSeAM), has a wide spectrum of reactivity against various lysine methyltransferases (KMTs) with sufficient stability to support enzymatic reactions in vitro. By using ProSeAM as a chemical probe for lysine methylation, we identified substrates for two seven-beta-strand KMTs, METTL21A and METTL10, on a proteomic scale in mammalian cells. METTL21A has been characterized as a heat shock protein (HSP)-70 methyltransferase. Mammalian METTL10 remains functionally uncharacterized, although its ortholog in yeast, See1, has been shown to methylate the translation elongation factor eEF1A. By using ProSeAM-mediated alkylation followed by purification and quantitative MS analysis, we confirmed that METTL21A labels HSP70 family proteins. Furthermore, we demonstrated that METTL10 also methylates the eukaryotic elongation factor EF1A1 in mammalian cells. Subsequent biochemical characterization revealed that METTL10 specifically trimethylates EF1A1 at lysine 318 and that siRNA-mediated knockdown of METTL10 decreases EF1A1 methylation levels in vivo. Thus, our study emphasizes the utility of the synthetic cofactor ProSeAM as a chemical probe for the identification of non-histone substrates of KMTs.
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Affiliation(s)
| | - Joaquin Barjau
- Synthetic Organic Chemistry Laboratory, RIKEN, Wako, Japan
| | | | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN, Wako, Japan
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106
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Zhang L, Hamey JJ, Hart-Smith G, Erce MA, Wilkins MR. Elongation factor methyltransferase 3--a novel eukaryotic lysine methyltransferase. Biochem Biophys Res Commun 2014; 451:229-34. [PMID: 25086354 DOI: 10.1016/j.bbrc.2014.07.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
Abstract
Here we describe the discovery of Saccharomycescerevisiae protein YJR129Cp as a new eukaryotic seven-beta-strand lysine methyltransferase. An immunoblotting screen of 21 putative methyltransferases showed a loss in the methylation of elongation factor 2 (EF2) on knockout of YJR129C. Mass spectrometric analysis of EF2 tryptic peptides localised this loss of methylation to lysine 509, in peptide LVEGLKR. In vitro methylation, using recombinant methyltransferases and purified EF2, validated YJR129Cp as responsible for methylation of lysine 509 and Efm2p as responsible for methylation at lysine 613. Contextualised on previously described protein structures, both sites of methylation were found at the interaction interface between EF2 and the 40S ribosomal subunit. In line with the recently discovered Efm1 and Efm2 we propose that YJR129C be named elongation factor methyltransferase 3 (Efm3). The human homolog of Efm3 is likely to be the putative methyltransferase FAM86A, according to sequence homology and multiple lines of literature evidence.
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Affiliation(s)
- Lelin Zhang
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Melissa A Erce
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia.
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107
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Rhein VF, Carroll J, He J, Ding S, Fearnley IM, Walker JE. Human METTL20 methylates lysine residues adjacent to the recognition loop of the electron transfer flavoprotein in mitochondria. J Biol Chem 2014; 289:24640-51. [PMID: 25023281 PMCID: PMC4148887 DOI: 10.1074/jbc.m114.580464] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mammalian mitochondria, protein methylation is a relatively uncommon post-transcriptional modification, and the extent of the mitochondrial protein methylome, the modifying methyltransferases, and their substrates have been little studied. As shown here, the β-subunit of the electron transfer flavoprotein (ETF) is one such methylated protein. The ETF is a heterodimer of α- and β-subunits. Lysine residues 199 and 202 of mature ETFβ are almost completely trimethylated in bovine heart mitochondria, whereas ETFα is not methylated. The enzyme responsible for the modifications was identified as methyltransferase-like protein 20 (METTL20). In human 143B cells, the methylation of ETFβ is less extensive and is diminished further by suppression of METTL20. Tagged METTL20 expressed in HEK293T cells specifically associates with the ETF and promotes the trimethylation of ETFβ lysine residues 199 and 202. ETF serves as a mobile electron carrier linking dehydrogenases involved in fatty acid oxidation and one-carbon metabolism to the membrane-associated ubiquinone pool. The methylated residues in ETFβ are immediately adjacent to a protein loop that recognizes and binds to the dehydrogenases. Suppression of trimethylation of ETFβ in mouse C2C12 cells oxidizing palmitate as an energy source reduced the consumption of oxygen by the cells. These experiments suggest that the oxidation of fatty acids in mitochondria and the passage of electrons via the ETF may be controlled by modulating the protein-protein interactions between the reduced dehydrogenases and the β-subunit of the ETF by trimethylation of lysine residues. METTL20 is the first lysine methyltransferase to be found to be associated with mitochondria.
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Affiliation(s)
- Virginie F Rhein
- From The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Joe Carroll
- From The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Jiuya He
- From The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Shujing Ding
- From The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Ian M Fearnley
- From The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - John E Walker
- From The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
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108
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Huang J, Hsu YH, Mo C, Abreu E, Kiel DP, Bonewald LF, Brotto M, Karasik D. METTL21C is a potential pleiotropic gene for osteoporosis and sarcopenia acting through the modulation of the NF-κB signaling pathway. J Bone Miner Res 2014; 29:1531-1540. [PMID: 24677265 PMCID: PMC4074268 DOI: 10.1002/jbmr.2200] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/31/2014] [Accepted: 02/04/2014] [Indexed: 01/06/2023]
Abstract
Sarcopenia and osteoporosis are important public health problems that occur concurrently. A bivariate genome-wide association study (GWAS) identified METTL21c as a suggestive pleiotropic gene for both bone and muscle. The METTL21 family of proteins methylates chaperones involved in the etiology of both myopathy and inclusion body myositis with Paget's disease. To validate these GWAS results, Mettl21c mRNA expression was reduced with siRNA in a mouse myogenic C2C12 cell line and the mouse osteocyte-like cell line MLO-Y4. At day 3, as C2C12 myoblasts start to differentiate into myotubes, a significant reduction in the number of myocytes aligning/organizing for fusion was observed in the siRNA-treated cells. At day 5, both fewer and smaller myotubes were observed in the siRNA-treated cells as confirmed by histomorphometric analyses and immunostaining with myosin heavy chain (MHC) antibody, which only stains myocytes/myotubes but not myoblasts. Intracellular calcium (Ca(2+)) measurements of the siRNA-treated myotubes showed a decrease in maximal amplitude peak response to caffeine, suggesting that less Ca(2+) is available for release due to the partial silencing of Mettl21c, correlating with impaired myogenesis. In siRNA-treated MLO-Y4 cells, 48 hours after treatment with dexamethasone there was a significant increase in cell death, suggesting a role of Mettl21c in osteocyte survival. To investigate the molecular signaling machinery induced by the partial silencing of Mettl21c, we used a real-time PCR gene array to monitor the activity of 10 signaling pathways. We discovered that Mettl21c knockdown modulated only the NF-κB signaling pathway (ie, Birc3, Ccl5, and Tnf). These results suggest that Mettl21c might exert its bone-muscle pleiotropic function via the regulation of the NF-κB signaling pathway, which is critical for bone and muscle homeostasis. These studies also provide rationale for cellular and molecular validation of GWAS, and warrant additional in vitro and in vivo studies to advance our understanding of role of METTL21C in musculoskeletal biology.
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Affiliation(s)
- Jian Huang
- Muscle Biology Research Group, Schools of Nursing & Health Studies, University of Missouri Kansas City, 2464 Charlotte Street, Kansas City, MO
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Chenglin Mo
- Muscle Biology Research Group, Schools of Nursing & Health Studies, University of Missouri Kansas City, 2464 Charlotte Street, Kansas City, MO
| | - Eduardo Abreu
- Muscle Biology Research Group, Schools of Nursing & Health Studies, University of Missouri Kansas City, 2464 Charlotte Street, Kansas City, MO
| | - Douglas P. Kiel
- Institute for Aging Research, Hebrew SeniorLife, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lynda F. Bonewald
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, MO, USA
| | - Maxrco Brotto
- Muscle Biology Research Group, Schools of Nursing & Health Studies, University of Missouri Kansas City, 2464 Charlotte Street, Kansas City, MO
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
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109
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Reiff RE, Ali BR, Baron B, Yu TW, Ben-Salem S, Coulter ME, Schubert CR, Hill RS, Akawi NA, Al-Younes B, Kaya N, Evrony GD, Al-Saffar M, Felie JM, Partlow JN, Sunu CM, Schembri-Wismayer P, Alkuraya FS, Meyer BF, Walsh CA, Al-Gazali L, Mochida GH. METTL23, a transcriptional partner of GABPA, is essential for human cognition. Hum Mol Genet 2014; 23:3456-66. [PMID: 24501276 PMCID: PMC4049305 DOI: 10.1093/hmg/ddu054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/12/2013] [Accepted: 01/31/2014] [Indexed: 02/06/2023] Open
Abstract
Whereas many genes associated with intellectual disability (ID) encode synaptic proteins, transcriptional defects leading to ID are less well understood. We studied a large, consanguineous pedigree of Arab origin with seven members affected with ID and mild dysmorphic features. Homozygosity mapping and linkage analysis identified a candidate region on chromosome 17 with a maximum multipoint logarithm of odds score of 6.01. Targeted high-throughput sequencing of the exons in the candidate region identified a homozygous 4-bp deletion (c.169_172delCACT) in the METTL23 (methyltransferase like 23) gene, which is predicted to result in a frameshift and premature truncation (p.His57Valfs*11). Overexpressed METTL23 protein localized to both nucleus and cytoplasm, and physically interacted with GABPA (GA-binding protein transcription factor, alpha subunit). GABP, of which GABPA is a component, is known to regulate the expression of genes such as THPO (thrombopoietin) and ATP5B (ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide) and is implicated in a wide variety of important cellular functions. Overexpression of METTL23 resulted in increased transcriptional activity at the THPO promoter, whereas knockdown of METTL23 with siRNA resulted in decreased expression of ATP5B, thus revealing the importance of METTL23 as a regulator of GABPA function. The METTL23 mutation highlights a new transcriptional pathway underlying human intellectual function.
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Affiliation(s)
- Rachel E Reiff
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences
| | - Byron Baron
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Timothy W Yu
- Division of Genetics and Genomics, Department of Medicine Department of Pediatrics Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Salma Ben-Salem
- Department of Pathology, College of Medicine and Health Sciences
| | - Michael E Coulter
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Christian R Schubert
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics Research Laboratory of Electronics and Department of Electrical Engineering and Computer Science, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Nadia A Akawi
- Department of Pathology, College of Medicine and Health Sciences
| | - Banan Al-Younes
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Gilad D Evrony
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Program in Biological and Biomedical Sciences and
| | - Muna Al-Saffar
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Jillian M Felie
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christine M Sunu
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pierre Schembri-Wismayer
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics Department of Neurology, Harvard Medical School, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Department of Pediatrics Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
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110
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Histidine methylation of yeast ribosomal protein Rpl3p is required for proper 60S subunit assembly. Mol Cell Biol 2014; 34:2903-16. [PMID: 24865971 DOI: 10.1128/mcb.01634-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histidine protein methylation is an unusual posttranslational modification. In the yeast Saccharomyces cerevisiae, the large ribosomal subunit protein Rpl3p is methylated at histidine 243, a residue that contacts the 25S rRNA near the P site. Rpl3p methylation is dependent upon the presence of Hpm1p, a candidate seven-beta-strand methyltransferase. In this study, we elucidated the biological activities of Hpm1p in vitro and in vivo. Amino acid analyses reveal that Hpm1p is responsible for all of the detectable protein histidine methylation in yeast. The modification is found on a polypeptide corresponding to the size of Rpl3p in ribosomes and in a nucleus-containing organelle fraction but was not detected in proteins of the ribosome-free cytosol fraction. In vitro assays demonstrate that Hpm1p has methyltransferase activity on ribosome-associated but not free Rpl3p, suggesting that its activity depends on interactions with ribosomal components. hpm1 null cells are defective in early rRNA processing, resulting in a deficiency of 60S subunits and translation initiation defects that are exacerbated in minimal medium. Cells lacking Hpm1p are resistant to cycloheximide and verrucarin A and have decreased translational fidelity. We propose that Hpm1p plays a role in the orchestration of the early assembly of the large ribosomal subunit and in faithful protein production.
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111
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O'Neill DJ, Williamson SC, Alkharaif D, Monteiro ICM, Goudreault M, Gaughan L, Robson CN, Gingras AC, Binda O. SETD6 controls the expression of estrogen-responsive genes and proliferation of breast carcinoma cells. Epigenetics 2014; 9:942-50. [PMID: 24751716 PMCID: PMC4143409 DOI: 10.4161/epi.28864] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The lysine methyltransferase SETD6 modifies the histone variant H2AZ, a key component of nuclear receptor-dependent transcription. Herein, we report the identification of several factors that associate with SETD6 and are implicated in nuclear hormone receptor signaling. Specifically, SETD6 associates with the estrogen receptor α (ERα), histone deacetylase HDAC1, metastasis protein MTA2, and the transcriptional co-activator TRRAP. Luciferase reporter assays identify SETD6 as a transcriptional repressor, in agreement with its association with HDAC1 and MTA2. However, SETD6 behaves as a co-activator of several estrogen-responsive genes, such as PGR and TFF1. Consistent with these results, silencing of SETD6 in several breast carcinoma cell lines induced cellular proliferation defects accompanied by enhanced expression of the cell cycle inhibitor CDKN1A and induction of apoptosis. Herein, we have identified several chromatin proteins that associate with SETD6 and described SETD6 as an essential factor for nuclear receptor signaling and cellular proliferation.
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Affiliation(s)
- Daniel J O'Neill
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | | | - Dhuha Alkharaif
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | | | - Marilyn Goudreault
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto, ON Canada
| | - Luke Gaughan
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | - Craig N Robson
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto, ON Canada; Department of Molecular Genetics; University of Toronto; Toronto, ON Canada
| | - Olivier Binda
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
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112
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Uncovering the protein lysine and arginine methylation network in Arabidopsis chloroplasts. PLoS One 2014; 9:e95512. [PMID: 24748391 PMCID: PMC3991674 DOI: 10.1371/journal.pone.0095512] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/27/2014] [Indexed: 11/28/2022] Open
Abstract
Post-translational modification of proteins by the addition of methyl groups to the side chains of Lys and Arg residues is proposed to play important roles in many cellular processes. In plants, identification of non-histone methylproteins at a cellular or subcellular scale is still missing. To gain insights into the extent of this modification in chloroplasts we used a bioinformatics approach to identify protein methyltransferases targeted to plastids and set up a workflow to specifically identify Lys and Arg methylated proteins from proteomic data used to produce the Arabidopsis chloroplast proteome. With this approach we could identify 31 high-confidence Lys and Arg methylation sites from 23 chloroplastic proteins, of which only two were previously known to be methylated. These methylproteins are split between the stroma, thylakoids and envelope sub-compartments. They belong to essential metabolic processes, including photosynthesis, and to the chloroplast biogenesis and maintenance machinery (translation, protein import, division). Also, the in silico identification of nine protein methyltransferases that are known or predicted to be targeted to plastids provided a foundation to build the enzymes/substrates relationships that govern methylation in chloroplasts. Thereby, using in vitro methylation assays with chloroplast stroma as a source of methyltransferases we confirmed the methylation sites of two targets, plastid ribosomal protein L11 and the β-subunit of ATP synthase. Furthermore, a biochemical screening of recombinant chloroplastic protein Lys methyltransferases allowed us to identify the enzymes involved in the modification of these substrates. The present study provides a useful resource to build the methyltransferases/methylproteins network and to elucidate the role of protein methylation in chloroplast biology.
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113
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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: 177] [Impact Index Per Article: 17.7] [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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114
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Bernkopf M, Webersinke G, Tongsook C, Koyani CN, Rafiq MA, Ayaz M, Müller D, Enzinger C, Aslam M, Naeem F, Schmidt K, Gruber K, Speicher MR, Malle E, Macheroux P, Ayub M, Vincent JB, Windpassinger C, Duba HC. Disruption of the methyltransferase-like 23 gene METTL23 causes mild autosomal recessive intellectual disability. Hum Mol Genet 2014; 23:4015-23. [PMID: 24626631 PMCID: PMC4082365 DOI: 10.1093/hmg/ddu115] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe the characterization of a gene for mild nonsyndromic autosomal recessive intellectual disability (ID) in two unrelated families, one from Austria, the other from Pakistan. Genome-wide single nucleotide polymorphism microarray analysis enabled us to define a region of homozygosity by descent on chromosome 17q25. Whole-exome sequencing and analysis of this region in an affected individual from the Austrian family identified a 5 bp frameshifting deletion in the METTL23 gene. By means of Sanger sequencing of METTL23, a nonsense mutation was detected in a consanguineous ID family from Pakistan for which homozygosity-by-descent mapping had identified a region on 17q25. Both changes lead to truncation of the putative METTL23 protein, which disrupts the predicted catalytic domain and alters the cellular localization. 3D-modelling of the protein indicates that METTL23 is strongly predicted to function as an S-adenosyl-methionine (SAM)-dependent methyltransferase. Expression analysis of METTL23 indicated a strong association with heat shock proteins, which suggests that these may act as a putative substrate for methylation by METTL23. A number of methyltransferases have been described recently in association with ID. Disruption of METTL23 presented here supports the importance of methylation processes for intact neuronal function and brain development.
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Affiliation(s)
- Marie Bernkopf
- Laboratory of Molecular Biology and Tumorcytogenetics, Department of Internal Medicine, Krankenhaus der Barmherzigen Schwestern, Linz, Austria
| | - Gerald Webersinke
- Laboratory of Molecular Biology and Tumorcytogenetics, Department of Internal Medicine, Krankenhaus der Barmherzigen Schwestern, Linz, Austria
| | - Chanakan Tongsook
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Chintan N Koyani
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Muhammad A Rafiq
- Molecular Neuropsychiatry and Development (MiND) Lab, The Campbell Family Brain Research Institute, The Centre for Addiction & Mental Health (CAMH), Toronto, ON, Canada
| | - Muhammad Ayaz
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan
| | - Doris Müller
- Department of Human Genetics, Landes-Frauen und Kinderklinik, Linz, Austria
| | | | - Muhammad Aslam
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan
| | - Farooq Naeem
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Kurt Schmidt
- Department of Pharmacology and Toxicology, Karl-Franzens University Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Ernst Malle
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Muhammad Ayub
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, The Campbell Family Brain Research Institute, The Centre for Addiction & Mental Health (CAMH), Toronto, ON, Canada Department of Psychiatry and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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115
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Abstract
Insulin regulates glucose uptake by controlling the subcellular location of GLUT4 glucose transporters. GLUT4 is sequestered within fat and muscle cells during low-insulin states, and is translocated to the cell surface upon insulin stimulation. The TUG protein is a functional tether that sequesters GLUT4 at the Golgi matrix. To stimulate glucose uptake, insulin triggers TUG endoproteolytic cleavage. Cleavage accounts for a large proportion of the acute effect of insulin to mobilize GLUT4 to the cell surface. During ongoing insulin exposure, endocytosed GLUT4 recycles to the plasma membrane directly from endosomes, and bypasses a TUG-regulated trafficking step. Insulin acts through the TC10α GTPase and its effector protein, PIST, to stimulate TUG cleavage. This action is coordinated with insulin signals through AS160/Tbc1D4 and Tbc1D1 to modulate Rab GTPases, and with other signals to direct overall GLUT4 targeting. Data support the idea that the N-terminal TUG cleavage product, TUGUL, functions as a novel ubiquitin-like protein modifier to facilitate GLUT4 movement to the cell surface. The C-terminal TUG cleavage product is extracted from the Golgi matrix, which vacates an "anchoring" site to permit subsequent cycles of GLUT4 retention and release. Together, GLUT4 vesicle translocation and TUG cleavage may coordinate glucose uptake with physiologic effects of other proteins present in the GLUT4-containing vesicles, and with potential additional effects of the TUG C-terminal product. Understanding this TUG pathway for GLUT4 retention and release will shed light on the regulation of glucose uptake and the pathogenesis of type 2 diabetes.
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Affiliation(s)
- Jonathan P Belman
- Section of Endocrinology and Metabolism, Department of Internal Medicine, and Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, Box 208020, New Haven, CT, 06520-8020, USA
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116
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Moore KE, Gozani O. An unexpected journey: lysine methylation across the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1395-403. [PMID: 24561874 DOI: 10.1016/j.bbagrm.2014.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/11/2014] [Indexed: 12/17/2022]
Abstract
The dynamic modification of histone proteins by lysine methylation has emerged over the last decade as a key regulator of chromatin functions. In contrast, our understanding of the biological roles for lysine methylation of non-histone proteins has progressed more slowly. Though recently it has attracted less attention, ε-methyl-lysine in non-histone proteins was first observed over 50 years ago. In that time, it has become clear that, like the case for histones, non-histone methylation represents a key and common signaling process within the cell. Recent work suggests that non-histone methylation occurs on hundreds of proteins found in both the nucleus and the cytoplasm, and with important biomedical implications. Technological advances that allow us to identify lysine methylation on a proteomic scale are opening new avenues in the non-histone methylation field, which is poised for dramatic growth. Here, we review historical and recent findings in non-histone lysine methylation signaling, highlight new methods that are expanding opportunities in the field, and discuss outstanding questions and future challenges about the role of this fundamental post-translational modification (PTM).
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Affiliation(s)
- Kaitlyn E Moore
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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117
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Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B. Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin. J Proteomics 2013; 100:115-24. [PMID: 24140279 DOI: 10.1016/j.jprot.2013.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/25/2013] [Accepted: 10/07/2013] [Indexed: 02/06/2023]
Abstract
UNLABELLED Kin17 is a protein that was discovered through its immunoreactivity towards an antibody directed against prokaryotic RecA. Further study of Kin17 revealed a function in DNA replication and repair, as well as in pre-mRNA processing. Recently, it was found that Kin17 is methylated on lysine 135 by the newly discovered methyltransferase METTL22. To better understand the function of Kin17 and its regulation by methylation, we used multiple cell compartment protein affinity purification coupled with mass spectrometry (MCC-AP-MS) to identify novel interaction partners of Kin17 and to assess whether these interactions can take place on chromatin. Our results confirm that Kin17 interacts with METTL22 both in the soluble and chromatin fractions. We also show that many RNA-binding proteins, including the previously identified interactor BUD13 as well as spliceosomal and ribosomal subunits, associate with Kin17 in the soluble fraction. Interestingly, overexpression of METTL22 in HEK 293 cells displaces Kin17 from the chromatin to the cytoplasmic fraction, suggesting a role for methylation of lysine 135, a residue that lies within a winged helix domain of Kin17, in regulating association with chromatin. These results are discussed in view of the putative cellular function of Kin17. BIOLOGICAL SIGNIFICANCE The results shown here broaden our understanding of METTL22, a member of a family of newly-discovered non-histone lysine methyltransferases and its substrate, Kin17, a DNA/RNA-binding protein with reported roles in DNA repair and replication and mRNA processing. An innovative method to study protein-protein interactions in multiple cell compartments is employed to outline the interaction network of both proteins. Functional experiments uncover a correlative role between Kin17 lysine methylation and its association with chromatin. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Mathieu Lavallée-Adam
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada; Department of Biochemistry, Université de Montréal, Montréal, Québec H3T 1J4, Canada.
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118
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Rhein VF, Carroll J, Ding S, Fearnley IM, Walker JE. NDUFAF7 methylates arginine 85 in the NDUFS2 subunit of human complex I. J Biol Chem 2013; 288:33016-26. [PMID: 24089531 PMCID: PMC3829151 DOI: 10.1074/jbc.m113.518803] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 subunits. One arm is embedded in the inner membrane with the other protruding ∼100 Å into the matrix of the organelle. The extrinsic arm contains binding sites for NADH and the primary electron acceptor FMN, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking FMN to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, probably energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Complex I is put together from preassembled subcomplexes. Their compositions have been characterized partially, and at least 12 extrinsic assembly factor proteins are required for the assembly of the complex. One such factor, NDUFAF7, is predicted to belong to the family of S-adenosylmethionine-dependent methyltransferases characterized by the presence in their structures of a seven-β-strand protein fold. In the present study, the presence of NDUFAF7 in the mitochondrial matrix has been confirmed, and it has been demonstrated that it is a protein methylase that symmetrically dimethylates the ω-NG,NG′ atoms of residue Arg-85 in the NDUFS2 subunit of complex I. This methylation step occurs early in the assembly of complex I and probably stabilizes a 400-kDa subcomplex that forms the initial nucleus of the peripheral arm and its juncture with the membrane arm.
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Affiliation(s)
- Virginie F Rhein
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
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119
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Cdc48: a swiss army knife of cell biology. JOURNAL OF AMINO ACIDS 2013; 2013:183421. [PMID: 24167726 PMCID: PMC3791797 DOI: 10.1155/2013/183421] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/29/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.
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120
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Jakobsson ME, Moen A, Bousset L, Egge-Jacobsen W, Kernstock S, Melki R, Falnes PØ. Identification and characterization of a novel human methyltransferase modulating Hsp70 protein function through lysine methylation. J Biol Chem 2013; 288:27752-63. [PMID: 23921388 DOI: 10.1074/jbc.m113.483248] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hsp70 proteins constitute an evolutionarily conserved protein family of ATP-dependent molecular chaperones involved in a wide range of biological processes. Mammalian Hsp70 proteins are subject to various post-translational modifications, including methylation, but for most of these, a functional role has not been attributed. In this study, we identified the methyltransferase METTL21A as the enzyme responsible for trimethylation of a conserved lysine residue found in several human Hsp70 (HSPA) proteins. This enzyme, denoted by us as HSPA lysine (K) methyltransferase (HSPA-KMT), was found to catalyze trimethylation of various Hsp70 family members both in vitro and in vivo, and the reaction was stimulated by ATP. Furthermore, we show that HSPA-KMT exclusively methylates 70-kDa proteins in mammalian protein extracts, demonstrating that it is a highly specific enzyme. Finally, we show that trimethylation of HSPA8 (Hsc70) has functional consequences, as it alters the affinity of the chaperone for both the monomeric and fibrillar forms of the Parkinson disease-associated protein α-synuclein.
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Affiliation(s)
- Magnus E Jakobsson
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway and
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121
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Abstract
Lysine methylation of histones and non-histone proteins has emerged in recent years as a posttranslational modification with wide-ranging cellular implications beyond epigenetic regulation. The molecular interactions between lysine methyltransferases and their substrates appear to be regulated by posttranslational modifications surrounding the lysine methyl acceptor. Two very interesting examples of this cross-talk between methyl-lysine sites are found in the SET (Su(var)3–9, Enhancer-of-zeste, Trithorax) domain-containing lysine methyltransferases SET7 and SETDB1, whereby the histone H3 trimethylated on lysine 4 (H3K4me3) modification prevents methylation by SETDB1 on H3 lysine 9 (H3K9) and the histone H3 trimethylated on lysine 9 (H3K9me3) modification prevents methylation by SET7 on H3K4. A similar cross-talk between posttranslational modifications regulates the functions of non-histone proteins such as the tumor suppressor p53 and the DNA methyltransferase DNMT1. Herein, in cis effects of acetylation, phosphorylation, as well as arginine and lysine methylation on lysine methylation events will be discussed.
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Affiliation(s)
- Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research; Newcastle University, Newcastle upon Tyne, England.
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122
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Joshi P, Quach OL, Giguere SSB, Cristea IM. A Functional Proteomics Perspective of DBC1 as a Regulator of Transcription. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2013; Suppl 2:002. [PMID: 24273392 PMCID: PMC3837576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The past few years have seen significant advances in the use of modern proteomics approaches for biological discoveries. Among the fields impacted by proteomics is that of epigenetics, as mass spectrometry-based approaches have allowed the identification and characterization of transcriptional regulators, epigenetic marks, and the constantly evolving epigenetic landscape of a cell in health and disease states. These studies have substantially expanded our understanding of critical genes that mediate cell processes, such as differentiation, cell cycle regulation, and apoptosis. Not surprisingly, a great emphasis has been placed on defining factors that are de-regulated in cancers, in an attempt to define new and specific targets for therapeutic design. Differential gene expression observed during carcinogenesis can be induced by aberrant activities of transcription factors and chromatin remodeling enzymes. Through a series of recent mass spectrometry studies of histone deacetylases and nuclear receptors, Deleted in Breast Cancer 1 (DBC1) has emerged as a master regulator of transcriptional processes. DBC1 acts as a modulator of cellular epigenetic mechanisms and is frequently associated with human metastasis. Through its negative regulation of SIRT1 and HDAC3 deacetylation activities, DBC1 has a broad impact on gene expression, downstream cellular pathways, and associated human diseases. Here, we review the identified roles of DBC1, highlighting the critical contribution of mass spectrometry to these findings. Additionally, we provide a perspective of integrative proteomics approaches that can continue to shed light on the interplay between DBC1 and its protein targets, helping to further define its role in epigenetic modifications and to identify novel targets for cancer therapy.
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Affiliation(s)
- P Joshi
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - O L Quach
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - S S B Giguere
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - I M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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123
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Cloutier P, Coulombe B. Regulation of molecular chaperones through post-translational modifications: decrypting the chaperone code. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:443-54. [PMID: 23459247 DOI: 10.1016/j.bbagrm.2013.02.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/30/2022]
Abstract
Molecular chaperones and their associated cofactors form a group of highly specialized proteins that orchestrate the folding and unfolding of other proteins and the assembly and disassembly of protein complexes. Chaperones are found in all cell types and organisms, and their activity must be tightly regulated to maintain normal cell function. Indeed, deregulation of protein folding and protein complex assembly is the cause of various human diseases. Here, we present the results of an extensive review of the literature revealing that the post-translational modification (PTM) of chaperones has been selected during evolution as an efficient mean to regulate the activity and specificity of these key proteins. Because the addition and reciprocal removal of chemical groups can be triggered very rapidly, this mechanism provides an efficient switch to precisely regulate the activity of chaperones on specific substrates. The large number of PTMs detected in chaperones suggests that a combinatory code is at play to regulate function, activity, localization, and substrate specificity for this group of biologically important proteins. This review surveys the core information currently available as a starting point toward the more ambitious endeavor of deciphering the "chaperone code".
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