1
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Vai A, Noberini R, Ghirardi C, Rodrigues de Paula D, Carminati M, Pallavi R, Araújo N, Varga-Weisz P, Bonaldi T. Improved Mass Spectrometry-based methods reveal abundant propionylation and tissue specific histone propionylation profiles. Mol Cell Proteomics 2024:100799. [PMID: 38866077 DOI: 10.1016/j.mcpro.2024.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024] Open
Abstract
Histone post-translational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry (MS) is the most powerful, comprehensive and unbiased method to study histone PTMs. However, typical MS-based protocols for histone PTM analysis do not allow identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues, also upon perturbation with antibiotics, and breast cancer samples from the normal counterpart. Our results show that profiling only classical modifications is limiting and highlight the importance of using sample preparation methods that allows the analysis of the widest possible spectrum of histone modifications, paving the way for deeper insights into their functional significance in cellular processes and disease states.
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Affiliation(s)
- Alessandro Vai
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCSS, 20139, Milan, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCSS, 20139, Milan, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCSS, 20139, Milan, Italy
| | - Dieggo Rodrigues de Paula
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Michele Carminati
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCSS, 20139, Milan, Italy
| | - Rani Pallavi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCSS, 20139, Milan, Italy
| | - Nathália Araújo
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Patrick Varga-Weisz
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil; São Paulo Excellence Chair, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil; School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCSS, 20139, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, 20122, Milan, Italy.
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2
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Spadaro A, Sharma A, Dehzangi I. Predicting lysine methylation sites using a convolutional neural network. Methods 2024; 226:127-132. [PMID: 38604414 DOI: 10.1016/j.ymeth.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/15/2023] [Accepted: 04/07/2024] [Indexed: 04/13/2024] Open
Abstract
Protein lysine methylation is a particular type of post translational modification that plays an important role in both histone and non-histone function regulation in proteins. Deregulation caused by lysine methyltransferases has been identified as the cause of several diseases including cancer as well as both mental and developmental disorders. Identifying lysine methylation sites is a critical step in both early diagnosis and drug design. This study proposes a new Machine Learning method called CNN-Meth for predicting lysine methylation sites using a convolutional neural network (CNN). Our model is trained using evolutionary, structural, and physicochemical-based presentation along with binary encoding. Unlike previous studies, instead of extracting handcrafted features, we use CNN to automatically extract features from different presentations of amino acids to avoid information loss. Automated feature extraction from these representations of amino acids as well as CNN as a classifier have never been used for this problem. Our results demonstrate that CNN-Meth can significantly outperform previous methods for predicting methylation sites. It achieves 96.0%, 85.1%, 96.4%, and 0.65 in terms of Accuracy, Sensitivity, Specificity, and Matthew's Correlation Coefficient (MCC), respectively. CNN-Meth and its source code are publicly available at https://github.com/MLBC-lab/CNN-Meth.
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Affiliation(s)
- Austin Spadaro
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Alok Sharma
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia; Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States; Department of Computer Science, Rutgers University, Camden, NJ, United States.
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3
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Emenike B, Czabala P, Farhi J, Swaminathan J, Anslyn EV, Spangle J, Raj M. Tertiary Amine Coupling by Oxidation for Selective Labeling of Dimethyl Lysine Post-Translational Modifications. J Am Chem Soc 2024; 146:10621-10631. [PMID: 38584362 PMCID: PMC11027136 DOI: 10.1021/jacs.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Lysine dimethylation (Kme2) is a crucial post-translational modification (PTM) that regulates biological processes and is implicated in diseases. There is significant interest in globally identifying these methylation marks. Unfortunately, this remains challenging due to the lack of robust technologies for selectively labeling Kme2. To address this, we present a chemical method named tertiary amine coupling by oxidation (TACO). This method selectively modifies Kme2 to aldehydes using Selectfluor and a base. The resulting aldehydes from Kme2 were then functionalized using reductive amination, thiolamine, and oxime chemistry. We successfully demonstrated the versatility of TACO in selectively labeling Kme2 peptides and proteins in complex cell lysate mixtures with varying payloads, including affinity tags and fluorophores. We further showed the application of TACO chemistry for the identification of Kme2 sites at a single-molecule level by fluorosequencing. We discovered novel 30 Kme2 sites, in addition to previously known 5 Kme2 sites, by proteomics analysis of TACO-modified nuclear extracts. Our work establishes a unique strategy for covalently modifying Kme2, facilitating the global identification of low-abundance Kme2-PTMs and their sites within complex cell lysate mixtures.
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Affiliation(s)
- Benjamin Emenike
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Patrick Czabala
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan Farhi
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Jagannath Swaminathan
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer Spangle
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Monika Raj
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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4
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Brown T, Nguyen T, Zhou B, Zheng YG. Chemical probes and methods for the study of protein arginine methylation. RSC Chem Biol 2023; 4:647-669. [PMID: 37654509 PMCID: PMC10467615 DOI: 10.1039/d3cb00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.
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Affiliation(s)
- Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Terry Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
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5
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Hamey JJ, Wilkins MR. The protein methylation network in yeast: A landmark in completeness for a eukaryotic post-translational modification. Proc Natl Acad Sci U S A 2023; 120:e2215431120. [PMID: 37252976 PMCID: PMC10265986 DOI: 10.1073/pnas.2215431120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Defining all sites for a post-translational modification in the cell, and identifying their upstream modifying enzymes, is essential for a complete understanding of a modification's function. However, the complete mapping of a modification in the proteome and definition of its associated enzyme-substrate network is rarely achieved. Here, we present the protein methylation network for Saccharomyces cerevisiae. Through a formal process of defining and quantifying all potential sources of incompleteness, for both the methylation sites in the proteome and also protein methyltransferases, we prove that this protein methylation network is now near-complete. It contains 33 methylated proteins and 28 methyltransferases, comprising 44 enzyme-substrate relationships, and a predicted further three enzymes. While the precise molecular function of most methylation sites is unknown, and it remains possible that other sites and enzymes remain undiscovered, the completeness of this protein modification network is unprecedented and allows us to holistically explore the role and evolution of protein methylation in the eukaryotic cell. We show that while no single protein methylation event is essential in yeast, the vast majority of methylated proteins are themselves essential, being primarily involved in the core cellular processes of transcription, RNA processing, and translation. This suggests that protein methylation in lower eukaryotes exists to fine-tune proteins whose sequences are evolutionarily constrained, providing an improvement in the efficiency of their cognate processes. The approach described here, for the construction and evaluation of post-translational modification networks and their constituent enzymes and substrates, defines a formal process of utility for other post-translational modifications.
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Affiliation(s)
- Joshua J. Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
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6
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Zhang X, Noberini R, Vai A, Bonaldi T, Seidl MF, Collemare J. Detection and quantification of the histone code in the fungal genus Aspergillus. Fungal Genet Biol 2023; 167:103800. [PMID: 37146898 DOI: 10.1016/j.fgb.2023.103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/30/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
In eukaryotes, the combination of different histone post-translational modifications (PTMs) - the histone code - impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in three fungal species belonging to three distinct taxonomic sections of the genus Aspergillus (Aspergillus niger, Aspergillus nidulans (two strains), and Aspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1, H3K79me2, and H4K31ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy.
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jérȏme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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7
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Wang Y, Bedford MT. Effectors and effects of arginine methylation. Biochem Soc Trans 2023; 51:725-734. [PMID: 37013969 PMCID: PMC10212539 DOI: 10.1042/bst20221147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
Arginine methylation is a ubiquitous and relatively stable post-translational modification (PTM) that occurs in three types: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA). Methylarginine marks are catalyzed by members of the protein arginine methyltransferases (PRMTs) family of enzymes. Substrates for arginine methylation are found in most cellular compartments, with RNA-binding proteins forming the majority of PRMT targets. Arginine methylation often occurs in intrinsically disordered regions of proteins, which impacts biological processes like protein-protein interactions and phase separation, to modulate gene transcription, mRNA splicing and signal transduction. With regards to protein-protein interactions, the major 'readers' of methylarginine marks are Tudor domain-containing proteins, although additional domain types and unique protein folds have also recently been identified as methylarginine readers. Here, we will assess the current 'state-of-the-art' in the arginine methylation reader field. We will focus on the biological functions of the Tudor domain-containing methylarginine readers and address other domains and complexes that sense methylarginine marks.
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Affiliation(s)
- Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
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8
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Wang Q, Yan X, Fu B, Xu Y, Li L, Chang C, Jia C. mNeuCode Empowers Targeted Proteome Analysis of Arginine Dimethylation. Anal Chem 2023; 95:3684-3693. [PMID: 36757215 DOI: 10.1021/acs.analchem.2c04648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Characterization of protein arginine dimethylation presents significant challenges due to its occurrence at the substoichiometric level. To enable a targeted MS/MS analysis of these dimethylation sites, we developed the mNeuCode (methyl-neutron-coding) tag by metabolically labeling methylarginine with stable isotopes during cell culture, which generated a diagnostic peak containing the NeuCode isotopologue signature in a high-resolution MS scan. A software tool, termed NeuCodeFinder, was developed for screening the NeuCode signatures in mass spectra. Therefore, a targeted MS/MS workflow was established for proteome-wide discovery of arginine dimethylation. The efficacy and utility were demonstrated by identifying 176 arginine dimethylation sites residing on 70 proteins in HeLa cells. Among them, 38% of the sites and 29% of the dimethylated proteins are novel, including five novel arginine dimethylation sites on the protein FAM98A, which is a substrate of protein arginine methyltransferase 1 (PRMT1). Our results show that deletion of FAM98A in HeLa cells suppressed cell migration, and importantly, dimethylation-deficient mutation suppressed this process as well. Therefore, the PRMT1-FAM98A pathway mediates cell migration possibly through dimethylation of these newly identified sites of FAM98A. Our study might drive the methodological shift from shotgun-based to targeted proteome analysis for interrogation of the substoichiometric biomolecules by using NeuCode-enabled techniques.
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Affiliation(s)
- Qianqian Wang
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xin Yan
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, China.,Xiong County Center for Disease Control and Prevention, Baoding 071000, China
| | - Bin Fu
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ying Xu
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Cheng Chang
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, China.,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Chenxi Jia
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, China
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9
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Berryhill CA, Hanquier JN, Doud EH, Cordeiro-Spinetti E, Dickson BM, Rothbart SB, Mosley AL, Cornett EM. Global lysine methylome profiling using systematically characterized affinity reagents. Sci Rep 2023; 13:377. [PMID: 36611042 PMCID: PMC9825382 DOI: 10.1038/s41598-022-27175-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/27/2022] [Indexed: 01/08/2023] Open
Abstract
Lysine methylation modulates the function of histone and non-histone proteins, and the enzymes that add or remove lysine methylation-lysine methyltransferases (KMTs) and lysine demethylases (KDMs), respectively-are frequently mutated and dysregulated in human diseases. Identification of lysine methylation sites proteome-wide has been a critical barrier to identifying the non-histone substrates of KMTs and KDMs and for studying functions of non-histone lysine methylation. Detection of lysine methylation by mass spectrometry (MS) typically relies on the enrichment of methylated peptides by pan-methyllysine antibodies. In this study, we use peptide microarrays to show that pan-methyllysine antibodies have sequence bias, and we evaluate how the differential selectivity of these reagents impacts the detection of methylated peptides in MS-based workflows. We discovered that most commercially available pan-Kme antibodies have an in vitro sequence bias, and multiple enrichment approaches provide the most comprehensive coverage of the lysine methylome. Overall, global lysine methylation proteomics with multiple characterized pan-methyllysine antibodies resulted in the detection of 5089 lysine methylation sites on 2751 proteins from two human cell lines, nearly doubling the number of reported lysine methylation sites in the human proteome.
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Affiliation(s)
- Christine A Berryhill
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jocelyne N Hanquier
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Bradley M Dickson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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10
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Liu L, Lin B, Yin S, Ball LE, Delaney JR, Long DT, Gan W. Arginine methylation of BRD4 by PRMT2/4 governs transcription and DNA repair. SCIENCE ADVANCES 2022; 8:eadd8928. [PMID: 36475791 PMCID: PMC9728970 DOI: 10.1126/sciadv.add8928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
BRD4 functions as an epigenetic reader and plays a crucial role in regulating transcription and genome stability. Dysregulation of BRD4 is frequently observed in various human cancers. However, the molecular details of BRD4 regulation remain largely unknown. Here, we report that PRMT2- and PRMT4-mediated arginine methylation is pivotal for BRD4 functions on transcription, DNA repair, and tumor growth. Specifically, PRMT2/4 interacts with and methylates BRD4 at R179, R181, and R183. This arginine methylation selectively controls a transcriptional program by promoting BRD4 recruitment to acetylated histones/chromatin. Moreover, BRD4 arginine methylation is induced by DNA damage and thereby promotes its binding to chromatin for DNA repair. Deficiency in BRD4 arginine methylation significantly suppresses tumor growth and sensitizes cells to BET inhibitors and DNA damaging agents. Therefore, our findings reveal an arginine methylation-dependent regulatory mechanism of BRD4 and highlight targeting PRMT2/4 for better antitumor effect of BET inhibitors and DNA damaging agents.
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Affiliation(s)
- Liu Liu
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Baicheng Lin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shasha Yin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lauren E. Ball
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joe R. Delaney
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - David T. Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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11
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Albizia lebbeck-mediated ZnO phytosynthesis and their non-antimicrobial and biocompatibility studies. APPLIED NANOSCIENCE 2022. [DOI: 10.1007/s13204-022-02725-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Global profiling of arginine dimethylation in regulating protein phase separation by a steric effect-based chemical-enrichment method. Proc Natl Acad Sci U S A 2022; 119:e2205255119. [PMID: 36256816 PMCID: PMC9618127 DOI: 10.1073/pnas.2205255119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein arginine methylation plays an important role in regulating protein functions in different cellular processes, and its dysregulation may lead to a variety of human diseases. Recently, arginine methylation was found to be involved in modulating protein liquid-liquid phase separation (LLPS), which drives the formation of different membraneless organelles (MLOs). Here, we developed a steric effect-based chemical-enrichment method (SECEM) coupled with liquid chromatography-tandem mass spectrometry to analyze arginine dimethylation (DMA) at the proteome level. We revealed by SECEM that, in mammalian cells, the DMA sites occurring in the RG/RGG motifs are preferentially enriched within the proteins identified in different MLOs, especially stress granules (SGs). Notably, global decrease of protein arginine methylation severely impairs the dynamic assembly and disassembly of SGs. By further profiling the dynamic change of DMA upon SG formation by SECEM, we identified that the most dramatic change of DMA occurs at multiple sites of RG/RGG-rich regions from several key SG-contained proteins, including G3BP1, FUS, hnRNPA1, and KHDRBS1. Moreover, both in vitro arginine methylation and mutation of the identified DMA sites significantly impair LLPS capability of the four different RG/RGG-rich regions. Overall, we provide a global profiling of the dynamic changes of protein DMA in the mammalian cells under different stress conditions by SECEM and reveal the important role of DMA in regulating protein LLPS and SG dynamics.
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13
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Wang Y, Li S, Chen J, Zhu H, Harsh BN, Boler DD, Dilger AC, Shike DW, Suman SP. Supranutritional Supplementation of Vitamin E Influences Myoglobin Post-Translational Modifications in Postmortem Beef Longissimus Lumborum Muscle. MEAT AND MUSCLE BIOLOGY 2022. [DOI: 10.22175/mmb.13541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modifications (PTM) in myoglobin (Mb) can influence fresh meat color stability. Dietary supplementation of vitamin E improves beef color stability by delaying lipid oxidation–induced Mb oxidation and influences proteome profile of postmortem beef skeletal muscles. Nonetheless, the influence of vitamin E on Mb PTM in postmortem beef skeletal muscles has yet to be investigated. Therefore, the objective of the current study was to examine the effect of dietary vitamin E on Mb PTM in postmortem beef longissimus lumborum muscle. Beef longissimus lumborum muscle samples (24 h postmortem) were obtained from the carcasses of 9 vitamin E–supplemented (VITE; 1,000 IU vitamin E diet/heifer·d−1for 89 d) and 9 control (CONT; no supplemental vitamin E) heifers. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used to separate Mb from other sarcoplasmic proteins of beef longissimus lumborum muscle. Tandem mass spectrometry identified multiple PTM (phosphorylation, acetylation, 4-hydroxynonenalalkylation, methylation, dimethylation, trimethylation, and carboxymethylation) in the protein bands (17 kDa) representing Mb. The amino acids susceptible to phosphorylation were threonine (T) and tyrosine (Y), whereas lysine (K) residues were prone to other PTM. The same sites of phosphorylation (T34, T67, Y103), carboxymethylation (K77, K78), and 4-hydroxynonenal alkylation (K77, K78, K79) were identified in Mb from CONT and VITE samples, indicating that these PTM were not influenced by the vitamin E supplementation in cattle. Nonetheless, differential occurrence of acetylation, methylation, dimethylation, and trimethylation were identified in Mb from CONT and VITE samples. Overall, a greater number of amino acids were modified in CONT than VITE, suggesting that the supplementation of vitamin E decreased thenumbers of post-translationally modified residues in Mb. Additionally, PTM at K87, K96, K98, and K102 were unique to CONT, whereas PTM at K118 were unique to VITE. These findings suggested that dietary supplementation of vitamin E in beef cattle might protect amino acid residues in Mb—especially those located spatially close to proximal histidine—from undergoing PTM, thereby improving Mb redox stability.
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Affiliation(s)
- Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | - Shuting Li
- University of Kentucky Department of Animal and Food Sciences
| | - Jing Chen
- University of Kentucky Proteomics Core Facility
| | - Haining Zhu
- University of Kentucky Proteomics Core Facility
| | - Bailey N. Harsh
- University of Illinois Urbana-Champaign Department of Animal Sciences
| | - Dustin D. Boler
- University of Illinois Urbana-Champaign Department of Animal Sciences
| | - Anna C. Dilger
- University of Illinois Urbana-Champaign Department of Animal Sciences
| | - Daniel W. Shike
- University of Illinois Urbana-Champaign Department of Animal Sciences
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14
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Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses. Microb Genom 2022; 8. [PMID: 36129736 PMCID: PMC9676040 DOI: 10.1099/mgen.0.000856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy.,Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy
| | - Jerome Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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15
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Emenike B, Nwajiobi O, Raj M. Covalent Chemical Tools for Profiling Post-Translational Modifications. Front Chem 2022; 10:868773. [PMID: 35860626 PMCID: PMC9289218 DOI: 10.3389/fchem.2022.868773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs); a process that involves the proteolytic processing or catalytic attachment of diverse functional groups onto proteins. These modifications modulate a host of biological activities and responses. Consequently, anomalous PTMs often correlate to a host of diseases, hence there is a need to detect these transformations, both qualitatively and quantitatively. One technique that has gained traction is the use of robust chemical strategies to label different PTMs. By utilizing the intrinsic chemical reactivity of the different chemical groups on the target amino acid residues, this strategy can facilitate the delineation of the overarching and inclusionary roles of these different modifications. Herein, we will discuss the current state of the art in post-translational modification analysis, with a direct focus on covalent chemical methods used for detecting them.
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16
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Massignani E, Giambruno R, Maniaci M, Nicosia L, Yadav A, Cuomo A, Raimondi F, Bonaldi T. ProMetheusDB: An In-Depth Analysis of the High-Quality Human Methyl-proteome. Mol Cell Proteomics 2022; 21:100243. [PMID: 35577067 PMCID: PMC9207298 DOI: 10.1016/j.mcpro.2022.100243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 01/01/2023] Open
Abstract
Protein arginine (R) methylation is a post-translational modification involved in various biological processes, such as RNA splicing, DNA repair, immune response, signal transduction, and tumor development. Although several advancements were made in the study of this modification by mass spectrometry, researchers still face the problem of a high false discovery rate. We present a dataset of high-quality methylations obtained from several different heavy methyl stable isotope labeling with amino acids in cell culture experiments analyzed with a machine learning–based tool and show that this model allows for improved high-confidence identification of real methyl-peptides. Overall, our results are consistent with the notion that protein R methylation modulates protein–RNA interactions and suggest a role in rewiring protein–protein interactions, for which we provide experimental evidence for a representative case (i.e., NONO [non-POU domain–containing octamer-binding protein]–paraspeckle component 1 [PSPC1]). Upon intersecting our R-methyl-sites dataset with the PhosphoSitePlus phosphorylation dataset, we observed that R methylation correlates differently with S/T-Y phosphorylation in response to various stimuli. Finally, we explored the application of heavy methyl stable isotope labeling with amino acids in cell culture to identify unconventional methylated residues and successfully identified novel histone methylation marks on serine 28 and threonine 32 of H3. The database generated, named ProMetheusDB, is freely accessible at https://bioserver.ieo.it/shiny/app/prometheusdb. hmSEEKER 2.0 identifies methyl-peptides from hmSILAC data through machine learning. Arginine methylation plays a role in modulating protein–protein interactions. Arginine methylations occur more frequently in proximity of phosphorylation sites. hmSEEKER 2.0 was used to identify methylations occurring on nonstandard amino acids.
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Affiliation(s)
- Enrico Massignani
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; European School of Molecular Medicine (SEMM), Milan, Italy
| | - Roberto Giambruno
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy; Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; European School of Molecular Medicine (SEMM), Milan, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Raimondi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Bio@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy.
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17
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Małecki JM, Davydova E, Falnes PØ. Protein methylation in mitochondria. J Biol Chem 2022; 298:101791. [PMID: 35247388 PMCID: PMC9006661 DOI: 10.1016/j.jbc.2022.101791] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Many proteins are modified by posttranslational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g., respiratory Complex I, citrate synthase, and the ATP synthase. In the present review, we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation and present an outlook for this emergent research field.
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Affiliation(s)
- Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
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18
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Sanchez-Bailon MP, Choi SY, Dufficy ER, Sharma K, McNee GS, Gunnell E, Chiang K, Sahay D, Maslen S, Stewart GS, Skehel JM, Dreveny I, Davies CC. Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair. Nat Commun 2021; 12:6313. [PMID: 34728620 PMCID: PMC8564520 DOI: 10.1038/s41467-021-26413-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/04/2021] [Indexed: 11/26/2022] Open
Abstract
Cross-talk between distinct protein post-translational modifications is critical for an effective DNA damage response. Arginine methylation plays an important role in maintaining genome stability, but how this modification integrates with other enzymatic activities is largely unknown. Here, we identify the deubiquitylating enzyme USP11 as a previously uncharacterised PRMT1 substrate, and demonstrate that the methylation of USP11 promotes DNA end-resection and the repair of DNA double strand breaks (DSB) by homologous recombination (HR), an event that is independent from another USP11-HR activity, the deubiquitylation of PALB2. We also show that PRMT1 is a ubiquitylated protein that it is targeted for deubiquitylation by USP11, which regulates the ability of PRMT1 to bind to and methylate MRE11. Taken together, our findings reveal a specific role for USP11 during the early stages of DSB repair, which is mediated through its ability to regulate the activity of the PRMT1-MRE11 pathway.
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Affiliation(s)
- Maria Pilar Sanchez-Bailon
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Soo-Youn Choi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elizabeth R Dufficy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Karan Sharma
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Gavin S McNee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Emma Gunnell
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Kelly Chiang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Debashish Sahay
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Clare C Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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19
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Jakobsson ME. Enzymology and significance of protein histidine methylation. J Biol Chem 2021; 297:101130. [PMID: 34461099 PMCID: PMC8446795 DOI: 10.1016/j.jbc.2021.101130] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells synthesize proteins using 20 standard amino acids and expand their biochemical repertoire through intricate enzyme-mediated post-translational modifications (PTMs). PTMs can either be static and represent protein editing events or be dynamically regulated as a part of a cellular response to specific stimuli. Protein histidine methylation (Hme) was an elusive PTM for over 5 decades and has only recently attracted considerable attention through discoveries concerning its enzymology, extent, and function. Here, we review the status of the Hme field and discuss the implications of Hme in physiological and cellular processes. We also review the experimental toolbox for analysis of Hme and discuss the strengths and weaknesses of different experimental approaches. The findings discussed in this review demonstrate that Hme is widespread across cells and tissues and functionally regulates key cellular processes such as cytoskeletal dynamics and protein translation. Collectively, the findings discussed here showcase Hme as a regulator of key cellular functions and highlight the regulation of this modification as an emerging field of biological research.
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20
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Noberini R, Savoia EO, Brandini S, Greco F, Marra F, Bertalot G, Pruneri G, McDonnell LA, Bonaldi T. Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clin Epigenetics 2021; 13:145. [PMID: 34315505 PMCID: PMC8317427 DOI: 10.1186/s13148-021-01120-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Increasing evidence linking epigenetic mechanisms and different diseases, including cancer, has prompted in the last 15 years the investigation of histone post-translational modifications (PTMs) in clinical samples. Methods allowing the isolation of histones from patient samples followed by the accurate and comprehensive quantification of their PTMs by mass spectrometry (MS) have been developed. However, the applicability of these methods is limited by the requirement for substantial amounts of material. RESULTS To address this issue, in this study we streamlined the protein extraction procedure from low-amount clinical samples and tested and implemented different in-gel digestion strategies, obtaining a protocol that allows the MS-based analysis of the most common histone PTMs from laser microdissected tissue areas containing as low as 1000 cells, an amount approximately 500 times lower than what is required by available methods. We then applied this protocol to breast cancer patient laser microdissected tissues in two proof-of-concept experiments, identifying differences in histone marks in heterogeneous regions selected by either morphological evaluation or MALDI MS imaging. CONCLUSIONS These results demonstrate that analyzing histone PTMs from very small tissue areas and detecting differences from adjacent tumor regions is technically feasible. Our method opens the way for spatial epi-proteomics, namely the investigation of epigenetic features in the context of tissue and tumor heterogeneity, which will be instrumental for the identification of novel epigenetic biomarkers and aberrant epigenetic mechanisms.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Evelyn Oliva Savoia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Brandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Greco
- Institute of Life Sciences, Sant'Anna School of Advanced Studies, 56127, Pisa, Italy
- Fondazione Pisana Per La Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy
| | - Francesca Marra
- Department of Pathology, Fondazione IRCCS-Istituto Nazionale Tumori, Milan, Italy
| | - Giovanni Bertalot
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology, Fondazione IRCCS-Istituto Nazionale Tumori, Milan, Italy
| | - Liam A McDonnell
- Fondazione Pisana Per La Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
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21
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Protein arginine methylation: from enigmatic functions to therapeutic targeting. Nat Rev Drug Discov 2021; 20:509-530. [PMID: 33742187 DOI: 10.1038/s41573-021-00159-8] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) are emerging as attractive therapeutic targets. PRMTs regulate transcription, splicing, RNA biology, the DNA damage response and cell metabolism; these fundamental processes are altered in many diseases. Mechanistically understanding how these enzymes fuel and sustain cancer cells, especially in specific metabolic contexts or in the presence of certain mutations, has provided the rationale for targeting them in oncology. Ongoing inhibitor development, facilitated by structural biology, has generated tool compounds for the majority of PRMTs and enabled clinical programmes for the most advanced oncology targets, PRMT1 and PRMT5. In-depth mechanistic investigations using genetic and chemical tools continue to delineate the roles of PRMTs in regulating immune cells and cancer cells, and cardiovascular and neuronal function, and determine which pathways involving PRMTs could be synergistically targeted in combination therapies for cancer. This research is enhancing our knowledge of the complex functions of arginine methylation, will guide future clinical development and could identify new clinical indications.
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22
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Zhang F, Kerbl-Knapp J, Rodriguez Colman MJ, Meinitzer A, Macher T, Vujić N, Fasching S, Jany-Luig E, Korbelius M, Kuentzel KB, Mack M, Akhmetshina A, Pirchheim A, Paar M, Rinner B, Hörl G, Steyrer E, Stelzl U, Burgering B, Eisenberg T, Pertschy B, Kratky D, Madl T. Global analysis of protein arginine methylation. CELL REPORTS METHODS 2021; 1:100016. [PMID: 35475236 PMCID: PMC9017121 DOI: 10.1016/j.crmeth.2021.100016] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/02/2021] [Accepted: 05/12/2021] [Indexed: 12/25/2022]
Abstract
Quantitative information about the levels and dynamics of post-translational modifications (PTMs) is critical for an understanding of cellular functions. Protein arginine methylation (ArgMet) is an important subclass of PTMs and is involved in a plethora of (patho)physiological processes. However, because of the lack of methods for global analysis of ArgMet, the link between ArgMet levels, dynamics, and (patho)physiology remains largely unknown. We utilized the high sensitivity and robustness of nuclear magnetic resonance (NMR) spectroscopy to develop a general method for the quantification of global protein ArgMet. Our NMR-based approach enables the detection of protein ArgMet in purified proteins, cells, organoids, and mouse tissues. We demonstrate that the process of ArgMet is a highly prevalent PTM and can be modulated by small-molecule inhibitors and metabolites and changes in cancer and during aging. Thus, our approach enables us to address a wide range of biological questions related to ArgMet in health and disease.
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Affiliation(s)
- Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Jakob Kerbl-Knapp
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Maria J. Rodriguez Colman
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8010 Graz, Austria
| | - Therese Macher
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Nemanja Vujić
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Sandra Fasching
- Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Evelyne Jany-Luig
- Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Melanie Korbelius
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Katharina B. Kuentzel
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Maximilian Mack
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Alena Akhmetshina
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Anita Pirchheim
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Margret Paar
- Otto-Loewi Research Center, Physiological Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Beate Rinner
- Division of Biomedical Research, Medical University of Graz, 8036 Graz, Austria
| | - Gerd Hörl
- Otto-Loewi Research Center, Physiological Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Ernst Steyrer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Ulrich Stelzl
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Boudewijn Burgering
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Tobias Eisenberg
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- Field of Excellence BioHealth – University of Graz, Graz, Austria
| | - Brigitte Pertschy
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- Field of Excellence BioHealth – University of Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
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23
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Emery-Corbin SJ, Hamey JJ, Ansell BRE, Balan B, Tichkule S, Stroehlein AJ, Cooper C, McInerney BV, Hediyeh-Zadeh S, Vuong D, Crombie A, Lacey E, Davis MJ, Wilkins MR, Bahlo M, Svärd SG, Gasser RB, Jex AR. Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia. Mol Biol Evol 2021; 37:3525-3549. [PMID: 32702104 PMCID: PMC7743719 DOI: 10.1093/molbev/msaa186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis-a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
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Affiliation(s)
- Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Swapnil Tichkule
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Crystal Cooper
- Central Analytical Research Facility (CARF), Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Bernie V McInerney
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Andrew Crombie
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, Australia.,Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Melissa J Davis
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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24
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Wang Y, Li S, Rentfrow G, Chen J, Zhu H, Suman SP. Myoglobin Post-Translational Modifications Influence Color Stability of Beef Longissimus Lumborum. MEAT AND MUSCLE BIOLOGY 2021. [DOI: 10.22175/mmb.11689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Post-translational modifications (PTM) of proteins play critical roles in biological processes. PTM of muscle proteins influence meat quality. Nonetheless, myoglobin (Mb) PTM and their impact on fresh beef color stability have not been characterized yet. Therefore, our objectives were to identify Mb PTM in beef longissimus lumborum muscle during postmortem aging and to characterize their influence on color stability. The longissimus lumborum muscles from 9 (n = 9) beef carcasses (24 h postmortem) were subjected to wet aging for 0, 7, 14, and 21 d. At the end of each wet-aging period, steaks were fabricated. One steak for analyses of PTM was immediately frozen at −80°C, whereas other steaks were assigned to refrigerated storage in the darkness under aerobic packaging. Instrumental color and biochemical attributes were evaluated on day 0, 3, or 6 of storage. Mb PTM were analyzed using two-dimensional electrophoresis and tandem mass spectrometry. Surface redness (a* value), color stability, and Mb concentration decreased (P < 0.05) upon aging. Gel image analyses identified 6 Mb spots with similar molecular weight (17 kDa) but different isoelectric pH. Tandem mass spectrometry identified multiple PTM (phosphorylation, methylation, carboxymethylation, acetylation, and 4-hydroxynonenal alkylation) in these 6 isoforms. The amino acids susceptible to phosphorylation were serine (S), threonine (T), and tyrosine, whereas other PTM were detected in lysine (K), arginine (R), and histidine residues. Additionally, distal histidine (position 64), critical to heme stability, was found to be alkylated. Overall, Mb PTM increased with aging. The aging-induced PTM, especially those occurring close to hydrophobic heme pocket, could disrupt Mb tertiary structure, influence heme affinity, and compromise oxygen binding capacity, leading to decreased color stability of fresh beef. Furthermore, PTM at K45, K47, and K87 were unique to Mb from non-aged beef, whereas PTM at R31, T51, K96, K98, S121, R139, and K147 were unique to Mb from aged counterparts, indicating that these Mb PTM could be used as novel biomarkers for fresh beef color stability.
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Affiliation(s)
- Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | - Shuting Li
- University of Kentucky Department of Animal and Food Sciences
| | - Gregg Rentfrow
- University of Kentucky Department of Animal and Food Sciences
| | - Jing Chen
- University of Kentucky Proteomics Core Facility
| | - Haining Zhu
- University of Kentucky Proteomics Core Facility
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25
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Morelli AP, Tortelli TC, Pavan ICB, Silva FR, Granato DC, Peruca GF, Pauletti BA, Domingues RR, Bezerra RMN, De Moura LP, Paes Leme AF, Chammas R, Simabuco FM. Metformin impairs cisplatin resistance effects in A549 lung cancer cells through mTOR signaling and other metabolic pathways. Int J Oncol 2021; 58:28. [PMID: 33846781 PMCID: PMC8041480 DOI: 10.3892/ijo.2021.5208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the leading cause of cancer‑associated death worldwide and exhibits intrinsic and acquired therapeutic resistance to cisplatin (CIS). The present study investigated the role of mTOR signaling and other signaling pathways after metformin (MET) treatment in control and cisplatin‑resistant A549 cells, mapping pathways and possible targets involved in CIS sensitivity. MTT, flow cytometry, clonogenic assay, western blotting, proteomic analysis using the Stable Isotope Labeling by Amino acids in Cell culture (SILAC) approach and reverse transcription‑quantitative PCR were performed. The results revealed that CIS treatment induced mTOR signaling pathway overactivation, and the mTOR status was restored by MET. MET and the mTOR inhibitor rapamycin (RAPA) decreased the viability in control and resistant cells, and decreased the cell size increase induced by CIS. In control cells, MET and RAPA decreased colony formation after 72 h and decreased IC50 values, potentiating the effects of CIS. Proteomics analysis revealed important pathways regulated by MET, including transcription, RNA processing and IL‑12‑mediated signaling. In CIS‑resistant cells, MET regulated the apoptotic process, oxidative stress and G2/M transition. Annexin 4 (ANXA4) and superoxide dismutase 2 (SOD2), involved in apoptosis and oxidative stress, respectively, were chosen to validate the SILAC analysis and may represent potential therapeutic targets for lung cancer treatment. In conclusion, the chemosensitizing and antiproliferative effects of MET were associated with mTOR signaling and with potential novel targets, such as ANXA4 and SOD2, in human lung cancer cells.
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Affiliation(s)
- Ana Paula Morelli
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, State University of Campinas, Limeira, SP 13484‑350, Brazil
| | - Tharcísio Citrângulo Tortelli
- Centro de Investigação Translacional em Oncologia, Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 04021‑001, Brazil
| | - Isadora Carolina Betim Pavan
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, State University of Campinas, Limeira, SP 13484‑350, Brazil
| | - Fernando Riback Silva
- Laboratory of Signaling Mechanisms, School of Pharmaceutical Sciences, State University of Campinas, Campinas, SP 13083‑871, Brazil
| | - Daniela Campos Granato
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP 13083‑970, Brazil
| | - Guilherme Francisco Peruca
- Exercise Cell Biology Laboratory, School of Applied Sciences, State University of Campinas, Limeira, SP 13484‑350, Brazil
| | - Bianca Alves Pauletti
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP 13083‑970, Brazil
| | - Romênia Ramos Domingues
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP 13083‑970, Brazil
| | - Rosangela Maria Neves Bezerra
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, State University of Campinas, Limeira, SP 13484‑350, Brazil
| | - Leandro Pereira De Moura
- Exercise Cell Biology Laboratory, School of Applied Sciences, State University of Campinas, Limeira, SP 13484‑350, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP 13083‑970, Brazil
| | - Roger Chammas
- Centro de Investigação Translacional em Oncologia, Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 04021‑001, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, State University of Campinas, Limeira, SP 13484‑350, Brazil
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26
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Nwajiobi O, Mahesh S, Streety X, Raj M. Selective Triazenation Reaction (STaR) of Secondary Amines for Tagging Monomethyl Lysine Post-Translational Modifications. Angew Chem Int Ed Engl 2021; 60:7344-7352. [PMID: 33354813 DOI: 10.1002/anie.202013997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/29/2020] [Indexed: 11/09/2022]
Abstract
Lysine monomethylation (Kme) is an impactful post-translational modification (PTM) responsible for regulating biological processes and implicated in diseases, thus there is great interest in identifying these methylation marks globally. However, the progress in this area has been challenging because the addition of a small methyl group on lysine leads to negligible change in the bulk, charge, and hydrophobicity. Herein, we report an empowering chemical technology selective triazenation reaction, which we term "STaR", of secondary amines using arene diazonium salts to achieve highly selective, rapid, and robust tagging of Kme peptides from a complex mixture under biocompatible conditions. Although the resulting triazene-linkage with Kme is stable, we highlight the efficient decoupling of the triazene-conjugate to afford unmodified starting components under mild conditions when desired. Our work establishes a unique chemoselective, traceless bioconjugation strategy for the selective enrichment of Kme PTMs.
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Affiliation(s)
- Ogonna Nwajiobi
- Present address: Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Sriram Mahesh
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA
| | - Xavier Streety
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA
| | - Monika Raj
- Present address: Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
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27
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Selective Triazenation Reaction (STaR) of Secondary Amines for Tagging Monomethyl Lysine Post‐Translational Modifications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Wang Q, Li Z, Zhou J, Wang Y, Wang K, Qin H, Ye M. Chemical Depletion of Histidine-Containing Peptides Allows Identification of More Low-Abundance Methylation Sites from Proteome Samples. J Proteome Res 2021; 20:2497-2505. [PMID: 33682419 DOI: 10.1021/acs.jproteome.0c00976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein methylation, especially that occurs on arginine and lysine residues, is one of the most important post-translational modifications involved in various cellular processes including RNA splicing, DNA repair, and so forth. Systematic analysis of protein methylation would facilitate the understanding of its regulatory mechanisms. Strong cation chromatography has been used to globally analyze arginine/lysine methylation at the proteome scale with good performance. However, the co-enriched histidine-containing peptides severely interfere with the detection of low-abundance methylpeptides. Here, we developed a novel chemical strategy which enabled almost complete depletion of histidine-containing peptides in the protein digest, thereby resulting in the identification of more low-abundance arginine/lysine methylpeptides. Totally, 333 arginine and lysine methylation forms from 207 proteins were identified in this study. Overall, the number of methylation identifications increased about 50% by using our new method. Data are available via ProteomeXchange with the identifier PXD023845.
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Affiliation(s)
- Qi Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouxian Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Musiani D, Massignani E, Cuomo A, Yadav A, Bonaldi T. Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry. Curr Protein Pept Sci 2021; 21:725-739. [PMID: 32338214 DOI: 10.2174/1389203721666200426232531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/27/2022]
Abstract
The absence of efficient mass spectrometry-based approaches for the large-scale analysis of protein arginine methylation has hindered the understanding of its biological role, beyond the transcriptional regulation occurring through histone modification. In the last decade, however, several technological advances of both the biochemical methods for methylated polypeptide enrichment and the computational pipelines for MS data analysis have considerably boosted this research field, generating novel insights about the extent and role of this post-translational modification. Here, we offer an overview of state-of-the-art approaches for the high-confidence identification and accurate quantification of protein arginine methylation by high-resolution mass spectrometry methods, which comprise the development of both biochemical and bioinformatics methods. The further optimization and systematic application of these analytical solutions will lead to ground-breaking discoveries on the role of protein methylation in biological processes.
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Affiliation(s)
- Daniele Musiani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
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30
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Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response. Nat Commun 2020; 11:2396. [PMID: 32409666 PMCID: PMC7224190 DOI: 10.1038/s41467-020-16271-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Protein arginine methyltransferases (PRMTs) regulate diverse biological processes and are increasingly being recognized for their potential as drug targets. Here we report the discovery of a potent, selective, and cell-active chemical probe for PRMT7. SGC3027 is a cell permeable prodrug, which in cells is converted to SGC8158, a potent, SAM-competitive PRMT7 inhibitor. Inhibition or knockout of cellular PRMT7 results in drastically reduced levels of arginine monomethylated HSP70 family stress-associated proteins. Structural and biochemical analyses reveal that PRMT7-driven in vitro methylation of HSP70 at R469 requires an ATP-bound, open conformation of HSP70. In cells, SGC3027 inhibits methylation of both constitutive and inducible forms of HSP70, and leads to decreased tolerance for perturbations of proteostasis including heat shock and proteasome inhibitors. These results demonstrate a role for PRMT7 and arginine methylation in stress response. Protein arginine methyltransferases (PRMTs) are increasingly recognized as potential therapeutic targets but PRMT7 remains an understudied member of this enzyme family. Here, the authors develop a chemical probe for PRMT7 and apply it to elucidate the role of PRMT7 in the cellular stress response.
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31
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Liu Z, Wang Q, Mao J, Wang K, Fang Z, Miao QR, Ye M. Comparative proteomic analysis of protein methylation provides insight into the resistance of hepatocellular carcinoma to 5-fluorouracil. J Proteomics 2020; 219:103738. [PMID: 32198070 DOI: 10.1016/j.jprot.2020.103738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/22/2020] [Accepted: 03/10/2020] [Indexed: 12/28/2022]
Abstract
Protein methylation is one of the common post-translational modifications involved in diverse biological processes including signal transduction, transcriptional regulation, DNA repairing, gene activation, gene repression, and RNA processing. Due to technique limitation, the investigation of protein methylation in cancer cells is not well achieved, which hinders our understanding of the contribution of protein methylation to drug resistance. In this study, we analyzed the methylproteomes of both 5-fluorouracil (5-Fu) resistant Bel/5-Fu cell line and its parental Bel cell line by employing SPE-SCX based label-free quantitative proteomics. We identified 313 methylation forms on 294 sites in Bel cells and 294 methylation forms on 260 sites in Bel/5-Fu cells with high localization confidence. In addition, we quantified 251 methylation forms and found that 77 methylation forms significantly changed. After normalizing with the protein abundance, the 89 methylation forms were determined with the significant changes in site stoichiometry. The sequence characteristics of these significantly changed methylation sites are different. Gene ontology analysis showed that these significantly changed methylated proteins mainly involved in the biological processes of translation and transcription. Together, our findings indicated that protein methylation occurring in hepatocellular carcinoma might play a critical role in requiring drug resistance. SIGNIFICANCE: The drug resistance acquired in cancer cells has been considered as a major challenge for the cancer treatment. Due to complexity, the molecular mechanisms are still largely unknown. Identifying the key markers will improve our understanding of the mechanisms and is crucial for the development of new therapeutic strategies to overcome resistance. To date, increasing number of proteomics and phosphoproteomics studies were reported to investigate the mechanisms of drug resistance. However, the methylproteomics studies related to drug resistance were not reported yet. Here, we performed the SPE-SCX based label-free quantitative proteomics to analyze the methylproteomes of both resistant cell line Bel/5-Fu and sensitive cell line Bel. Through the qualitative and quantitative analysis, we found that the sequence characteristics of methylation sites were evidently different between these two cell lines. The results suggested that some methyltransferases might play a crucial role in the regulation of drug resistance. We also performed the analysis of methyl-site stoichiometry by normalizing the protein abundances. It was found that 89 methylation forms were determined with the significant changes in site stoichiometry, which may contribute to the development of the Bel cells into resistant cells. Our methylproteomes dataset would be useful to reveal novel molecular mechanisms of drug resistance acquired in hepatocellular carcinoma.
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Affiliation(s)
- Zhen Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing R Miao
- Divisions of Pediatric Surgery and Pediatric Pathology, Departments of Surgery and Pathology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY 11501, USA.
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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32
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Morettin A, Bourassa J, Mahadevan K, Trinkle-Mulcahy L, Cote J. Using affinity purification coupled with stable isotope labeling by amino acids in cell culture quantitative mass spectrometry to identify novel interactors/substrates of protein arginine methyltransferases. Methods 2020; 175:44-52. [PMID: 31794835 DOI: 10.1016/j.ymeth.2019.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
The protein arginine methyltransferase family (PRMT) is known as being the catalytic driving force for arginine methylation. This specific type of post translational modification is extensively used in biological processes, and therefore is highly relevant in the pathology of a profusion of diseases. Since altered PRMT expression or deregulation has been shown to contribute to a vast range of those diseases including cancer, their study is of great interest. Although an increasing number of substrates are being discovered for each PRMT, large scale proteomic methods can be used to identify novel interactors/substrates, further elucidating the role that PRMTs perform in physiological or disease states. Here, we describe the use of affinity purification (AP) coupled with stable isotope labeling with amino acids in cell culture (SILAC) quantitative mass spectrometry (MS) to identify protein interactors and substrates of PRMTs. We also explore the possibility of exploiting the fact most PRMTs display lower dissociation rates with their hypomethylated substrates as a strategy to increase the proportion of substrates identified in AP/MS studies.
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Affiliation(s)
- Alan Morettin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie Bourassa
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kohila Mahadevan
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jocelyn Cote
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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33
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Protein lysine methylation in the regulation of anoxia tolerance in the red eared slider turtle, Trachemys scripta elegans. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100660. [PMID: 32066095 DOI: 10.1016/j.cbd.2020.100660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/23/2022]
Abstract
The red eared slider turtle (Trachemys scripta elegans) is a champion vertebrate facultative anaerobe, capable of surviving for several months under conditions of exceptionally low oxygen availability. The ability of the turtle to facilitate this impressive tolerance to oxygen restriction is accomplished through a dramatic reduction in non-essential cellular processes. This is done in an attempt to conserve limited ATP stores and match demand in the anoxic state, with ATP supplied primarily through anaerobic glycolysis. Determining both the non-essential and the essential cellular processes that are deemed to be anoxia-responsive in the turtle has been an intense area of study over the past few decades. As a result, recent advancements have established the influence of global metabolic controls, such as post-transcriptional and post-translational regulation of gene expression in anoxia adaptation. A remaining question is whether or not epigenetic-level regulatory mechanisms are also utilized to allow for local control over gene expression. Recently, research has begun to document lysine methylation as an anoxia-responsive post-translational histone modification, as the activities of a number of methyl-lysine regulatory enzymes are extraordinarily sensitive to oxygen availability. As a result, oxygen-dependent methyl-lysine regulatory enzymes have been of particular interest to several recent studies of animal oxygen sensitivity, including the freshwater turtle. This review will introduce the concept of lysine methylation as an oxygen-sensitive protein modification as well as a prospectus on how this modification may contribute to anoxia tolerance in the turtle.
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Cornett EM, Ferry L, Defossez PA, Rothbart SB. Lysine Methylation Regulators Moonlighting outside the Epigenome. Mol Cell 2020; 75:1092-1101. [PMID: 31539507 DOI: 10.1016/j.molcel.2019.08.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023]
Abstract
Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases. Since then, the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass-spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.
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Affiliation(s)
- Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Laure Ferry
- Université de Paris, Epigenetics and Cell Fate, CNRS, 75013 Paris, France
| | | | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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Spadotto V, Giambruno R, Massignani E, Mihailovich M, Maniaci M, Patuzzo F, Ghini F, Nicassio F, Bonaldi T. PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic Acids Res 2020; 48:96-115. [PMID: 31777917 PMCID: PMC6943135 DOI: 10.1093/nar/gkz1051] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 10/04/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNA (miRNA) biogenesis is a tightly controlled multi-step process operated in the nucleus by the activity of the Microprocessor and its associated proteins. Through high resolution mass spectrometry (MS)- proteomics we discovered that this complex is extensively methylated, with 84 methylated sites associated to 19 out of its 24 subunits. The majority of the modifications occurs on arginine (R) residues (61), leading to 81 methylation events, while 30 lysine (K)-methylation events occurs on 23 sites of the complex. Interestingly, both depletion and pharmacological inhibition of the Type-I Protein Arginine Methyltransferases (PRMTs) lead to a widespread change in the methylation state of the complex and induce global decrease of miRNA expression, as a consequence of the impairment of the pri-to-pre-miRNA processing step. In particular, we show that the reduced methylation of the Microprocessor subunit ILF3 is linked to its diminished binding to the pri-miRNAs miR-15a/16, miR-17-92, miR-301a and miR-331. Our study uncovers a previously uncharacterized role of R-methylation in the regulation of miRNA biogenesis in mammalian cells.
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Affiliation(s)
- Valeria Spadotto
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Giambruno
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesca Patuzzo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Ghini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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36
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Musiani D, Giambruno R, Massignani E, Ippolito MR, Maniaci M, Jammula S, Manganaro D, Cuomo A, Nicosia L, Pasini D, Bonaldi T. PRMT1 Is Recruited via DNA-PK to Chromatin Where It Sustains the Senescence-Associated Secretory Phenotype in Response to Cisplatin. Cell Rep 2020; 30:1208-1222.e9. [DOI: 10.1016/j.celrep.2019.12.061] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/02/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
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Sarthou MCM, Revel BH, Villiers F, Alban C, Bonnot T, Gigarel O, Boisson AM, Ravanel S, Bourguignon J. Development of a metalloproteomic approach to analyse the response of Arabidopsis cells to uranium stress. Metallomics 2020; 12:1302-1313. [DOI: 10.1039/d0mt00092b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Elaboration of a top-down proteomic, biochemical and ionoproteomic toolbox to gain insights into the impact of uranyl (U) on Arabidopsis cells.
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38
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Yan X, Li L, Jia C. Discovery of Missing Methylation Sites on Endogenous Peptides of Human Cell Lines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2537-2547. [PMID: 31429054 PMCID: PMC7316123 DOI: 10.1007/s13361-019-02270-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Methylation of proteins has considerable impacts on physiological processes including signal transduction, DNA damage repair, transcriptional regulation, gene activation, and inhibition of gene expression. However, the traditional proteomics-based approach suffers from limited identification rates of these critical methylation sites on endogenous peptides. In this work, a peptidomics-based workflow was established to discover and characterize the global methylome of endogenous peptides in human cells. The reliability of our strategy was validated by methyl-SILAC labeling, resulting in 83% true-positive identifications in the HeLa cell line. We applied this approach to seven human cell lines, and 700 methylated forms on 646 putative methylation sites were identified in total, with over 61% of the methylation sites being newly identified. This study provides a complementary strategy for a traditional proteomics-based approach that enables identification of missing methylation sites and creates a first methylome draft of endogenous peptides of human cell lines, offering a valuable resource for in-depth studies of biological functions of methylated endogenous peptides.
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Affiliation(s)
- Xin Yan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Lingjun Li
- School of Life Sciences, Tianjin University, Tianjin, 300072, China.
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705, USA.
| | - Chenxi Jia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.
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39
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Pieroni L, Iavarone F, Olianas A, Greco V, Desiderio C, Martelli C, Manconi B, Sanna MT, Messana I, Castagnola M, Cabras T. Enrichments of post-translational modifications in proteomic studies. J Sep Sci 2019; 43:313-336. [PMID: 31631532 DOI: 10.1002/jssc.201900804] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
More than 300 different protein post-translational modifications are currently known, but only a few have been extensively investigated because modified proteoforms are commonly present in sub-stoichiometry amount. For this reason, improvement of specific enrichment techniques is particularly useful for the proteomic characterization of post-translationally modified proteins. Enrichment proteomic strategies could help the researcher in the challenging issue to decipher the complex molecular cross-talk existing between the different factors influencing the cellular pathways. In this review the state of art of the platforms applied for the enrichment of specific and most common post-translational modifications, such as glycosylation and glycation, phosphorylation, sulfation, redox modifications (i.e. sulfydration and nitrosylation), methylation, acetylation, and ubiquitinylation, are described. Enrichments strategies applied to characterize less studied post-translational modifications are also briefly discussed.
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Affiliation(s)
- Luisa Pieroni
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Viviana Greco
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudia Desiderio
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Irene Messana
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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40
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Hartel NG, Chew B, Qin J, Xu J, Graham NA. Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets. Mol Cell Proteomics 2019; 18:2149-2164. [PMID: 31451547 PMCID: PMC6823857 DOI: 10.1074/mcp.ra119.001625] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 01/02/2023] Open
Abstract
Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post-translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied because of the lack of robust, well-characterized techniques for methyl peptide enrichment. Here, to better investigate protein methylation, we compared two methods for methyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Using both methods, we identified 1720 methylation sites on 778 proteins. Comparison of these methods revealed that they are largely orthogonal, suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we then investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1). PRMT1 knockdown resulted in significant changes to 127 arginine methylation sites on 78 proteins. In contrast, only a single lysine methylation site was significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, we found 114 MMA sites that were either significantly downregulated or upregulated on proteins enriched for mRNA metabolic processes. PRMT1 knockdown also induced significant changes in both asymmetric dimethyl arginine (ADMA) and symmetric dimethyl arginine (SDMA). Using characteristic neutral loss fragmentation ions, we annotated dimethylarginines as either ADMA or SDMA. Through integrative analysis of methyl forms, we identified 18 high confidence PRMT1 substrates and 12 methylation sites that are scavenged by other non-PRMT1 arginine methyltransferases in the absence of PRMT1 activity. We also identified one methylation site, HNRNPA1 R206, which switched from ADMA to SDMA upon PRMT1 knockdown. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques to identify novel PRMT1 methylation targets and highlight the dynamic interplay between methyltransferases in mammalian cells.
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Affiliation(s)
- Nicolas G Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089
| | - Brandon Chew
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089
| | - Jian Qin
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California 90089; Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California 90089; Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089.
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41
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Lund PJ, Lehman SM, Garcia BA. Quantitative analysis of global protein lysine methylation by mass spectrometry. Methods Enzymol 2019; 626:475-498. [PMID: 31606088 DOI: 10.1016/bs.mie.2019.07.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Since protein activity is often regulated by posttranslational modifications, the qualitative and quantitative analysis of modification sites is critical for understanding the regulation of biological pathways that control cell function and phenotype. Methylation constitutes one of the many types of posttranslational modifications that target lysine residues. Although lysine methylation is perhaps most commonly associated with histone proteins and the epigenetic regulation of processes involving chromatin, methylation has also been observed as an important regulatory modification on other proteins, which has spurred the development of methods to profile lysine methylation sites more globally. As with many posttranslational modifications, tandem mass spectrometry represents an ideal platform for the high-throughput analysis of lysine methylation due to its high sensitivity and resolving power. The following protocol outlines a general method to assay lysine methylation across the proteome using SILAC and quantitative proteomics. First, cells are labeled by SILAC to allow for relative quantitation across different experimental conditions, such as cells with or without ectopic expression of a methyltransferase. Next, cells are lysed and proteins are digested into peptides. Methylated peptides are then enriched by immunoprecipitation with pan-specific antibodies against methylated lysine. Finally, the enriched peptides are analyzed by LC-MS/MS to identify methylated peptides and their modification sites and to compare the relative abundance of methylation events between different conditions. This approach should yield detection of a couple hundred lysine methylation sites, and those showing differential abundance may then be prioritized for further study.
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Affiliation(s)
- Peder J Lund
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Stephanie M Lehman
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, Smilow Center for Translational Research, University of Pennsylvania School of Medicine, Philadelphia, PA, United States.
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42
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Dilworth D, Barsyte-Lovejoy D. Targeting protein methylation: from chemical tools to precision medicines. Cell Mol Life Sci 2019; 76:2967-2985. [PMID: 31104094 PMCID: PMC11105543 DOI: 10.1007/s00018-019-03147-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
The methylation of proteins is integral to the execution of many important biological functions, including cell signalling and transcriptional regulation. Protein methyltransferases (PMTs) are a large class of enzymes that carry out the addition of methyl marks to a broad range of substrates. PMTs are critical for normal cellular physiology and their dysregulation is frequently observed in human disease. As such, PMTs have emerged as promising therapeutic targets with several inhibitors now in clinical trials for oncology indications. The discovery of chemical inhibitors and antagonists of protein methylation signalling has also profoundly impacted our general understanding of PMT biology and pharmacology. In this review, we present general principles for drugging protein methyltransferases or their downstream effectors containing methyl-binding modules, as well as best-in-class examples of the compounds discovered and their impact both at the bench and in the clinic.
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Affiliation(s)
- David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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43
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Jang KH, Yoon HN, Lee J, Yi H, Park SY, Lee SY, Lim Y, Lee HJ, Cho JW, Paik YK, Hancock WS, Ku NO. Liver disease-associated keratin 8 and 18 mutations modulate keratin acetylation and methylation. FASEB J 2019; 33:9030-9043. [PMID: 31199680 DOI: 10.1096/fj.201800263rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Keratin 8 (K8) and keratin 18 (K18) are the intermediate filament proteins whose phosphorylation/transamidation associate with their aggregation in Mallory-Denk bodies found in patients with various liver diseases. However, the functions of other post-translational modifications in keratins related to liver diseases have not been fully elucidated. Here, using a site-specific mutation assay combined with nano-liquid chromatography-tandem mass spectrometry, we identified K8-Lys108 and K18-Lys187/426 as acetylation sites, and K8-Arg47 and K18-Arg55 as methylation sites. Keratin mutation (Arg-to-Lys/Ala) at the methylation sites, but not the acetylation sites, led to decreased stability of the keratin protein. We compared keratin acetylation/methylation in liver disease-associated keratin variants. The acetylation of K8 variants increased or decreased to various extents, whereas the methylation of K18-del65-72 and K18-I150V variants increased. Notably, the highly acetylated/methylated K18-I150V variant was less soluble and exhibited unusually prolonged protein stability, which suggests that additional acetylation of highly methylated keratins has a synergistic effect on prolonged stability. Therefore, the different levels of acetylation/methylation of the liver disease-associated variants regulate keratin protein stability. These findings extend our understanding of how disease-associated mutations in keratins modulate keratin acetylation and methylation, which may contribute to disease pathogenesis.-Jang, K.-H., Yoon, H.-N., Lee, J., Yi, H., Park, S.-Y., Lee, S.-Y., Lim, Y., Lee, H.-J., Cho, J.-W., Paik, Y.-K., Hancock, W. S., Ku, N.-O. Liver disease-associated keratin 8 and 18 mutations modulate keratin acetylation and methylation.
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Affiliation(s)
- Kwi-Hoon Jang
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Han-Na Yoon
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Jongeun Lee
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Hayan Yi
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Sang-Yoon Park
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - So-Young Lee
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Younglan Lim
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Hyoung-Joo Lee
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Jin-Won Cho
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Young-Ki Paik
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Williams S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Nam-On Ku
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea.,Department of Bio-Convergence Integrated Science and Engineering Division, Underwood International College, Yonsei University, Seoul, Korea
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44
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Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T. Proteomics profiling of arginine methylation defines PRMT5 substrate specificity. Sci Signal 2019; 12:12/575/eaat8388. [PMID: 30940768 DOI: 10.1126/scisignal.aat8388] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze arginine methylation on both chromatin-bound and cytoplasmic proteins. Accumulating evidence supports the involvement of PRMT5, the major type II PRMT, in cell survival and differentiation pathways that are important during development and in tumorigenesis. PRMT5 is an attractive drug target in various cancers, and inhibitors are currently in oncological clinical trials. Nonetheless, given the complex biology of PRMT5 and its multiple nonhistone substrates, it is paramount to fully characterize these dynamic changes in methylation and to link them to the observed anticancer effects to fully understand the functions of PRMT5 and the consequences of its inhibition. Here, we used a newly established pipeline coupling stable isotope labeling with amino acids in cell culture (SILAC) with immunoenriched methyl peptides to globally profile arginine monomethylation and symmetric dimethylation after PRMT5 inhibition by a selective inhibitor. We adopted heavy methyl SILAC as an orthogonal validation method to reduce the false discovery rate. Through in vitro methylation assays, we validated a set of PRMT5 targets identified by mass spectrometry and provided previously unknown mechanistic insights into the preference of the enzyme to methylate arginine sandwiched between two neighboring glycines (a Gly-Arg-Gly, or "GRG," sequence). Our analysis led to the identification of previously unknown PRMT5 substrates, thus both providing insight into the global effects of PRMT5 and its inhibition in live cells, beyond chromatin, and refining our knowledge of its substrate specificity.
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Affiliation(s)
- Daniele Musiani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Liling Wu
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Marica Rosaria Ippolito
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Umut Ozbek
- Department of Population Health Science and Policy, Mount Sinai, New York, NY 10029, USA.,Tisch Cancer Institute, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Habiba Zorgati
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
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45
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A new chromatographic approach to analyze methylproteome with enhanced lysine methylation identification performance. Anal Chim Acta 2019; 1068:111-119. [PMID: 31072472 DOI: 10.1016/j.aca.2019.03.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 11/22/2022]
Abstract
Arginine/lysine methylation is an important post-translational modification (PTM) involved in DNA repairing, transcriptional regulation, etc. Immunoaffinity enrichment is currently the most widely used methods for the methylproteome analysis. Large-scale analysis of arginine methylation has been realized by using pan-R-methyl antibodies. Unfortunately, pan specific antibodies targeting all three lysine methylation forms are not available. In this study, we presented a novel chromatography-based enrichment method for global methylproteome analysis. The offline multidimensional tandem chromatography combining strong cation exchange (SCX) chromatography, immobilized metal ion affinity chromatography (IMAC) and high-pH reversed-phase chromatography (high-pH RP) was applied in the large-scale analysis of methylproteome. Totally, 860 forms on 765 sites were identified from BEL cells, covering all five arginine/lysine methylation forms. Among them, 27.21% were lysine methylation forms. This technique allows the simultaneous analysis of both arginine and lysine methylation while it has improved performance for the identification of lysine methylation. Therefore, it is a promising strategy for the investigation of biological functions related to methylation.
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46
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Federico A, Sepe R, Cozzolino F, Piccolo C, Iannone C, Iacobucci I, Pucci P, Monti M, Fusco A. The complex CBX7-PRMT1 has a critical role in regulating E-cadherin gene expression and cell migration. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:509-521. [PMID: 30826432 DOI: 10.1016/j.bbagrm.2019.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 11/17/2022]
Abstract
The Chromobox protein homolog 7 (CBX7) belongs to the Polycomb Group (PcG) family, and, as part of the Polycomb repressive complex (PRC1), contributes to maintain transcriptional gene repression. Loss of CBX7 expression has been reported in several human malignant neoplasias, where it often correlates with an advanced cancer state and poor survival, proposing CBX7 as a candidate tumor-suppressor gene in cancer progression. Indeed, CBX7 is able to positively or negatively regulate the expression of genes involved in cell proliferation and cancer progression, such as E-cadherin, cyclin E, osteopontin, EGR1. To understand the molecular mechanisms that underlie the involvement of CBX7 in cancer progression, we designed a functional proteomic experiment based on CHIP-MS to identify novel CBX7 protein partners. Among the identified CBX7-interacting proteins we focused our attention on the Protein Arginine Methyltransferase 1 (PRMT1) whose critical role in epithelial-mesenchymal transition (EMT), cancer cell migration and invasion has been already reported. We confirmed the interaction between CBX7 and PRMT1 and demonstrated that this interaction is crucial for PRMT1 enzymatic activity both in vitro and in vivo and for the regulation of E-cadherin expression, an important hallmark of EMT. These results suggest a general mechanism by which CBX7 interacting with histone modification enzymes like HDAC2 and PRMT1 enhances E-cadherin expression. Therefore, disruption of this equilibrium may induce impairment of E-cadherin expression and increased cell migration eventually leading to EMT and, then, cancer progression.
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Affiliation(s)
- Antonella Federico
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Romina Sepe
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Flora Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II" and CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Claudia Piccolo
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Carla Iannone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II" and CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Ilaria Iacobucci
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II" and CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Piero Pucci
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II" and CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Maria Monti
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II" and CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.
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47
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Massignani E, Cuomo A, Musiani D, Jammula S, Pavesi G, Bonaldi T. hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data. Proteomics 2019; 19:e1800300. [DOI: 10.1002/pmic.201800300] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/14/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Enrico Massignani
- Department of Experimental Oncology; IEO; European Institute of Oncology IRCCS; Milan Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology; IEO; European Institute of Oncology IRCCS; Milan Italy
| | - Daniele Musiani
- Department of Experimental Oncology; IEO; European Institute of Oncology IRCCS; Milan Italy
| | - SriGanesh Jammula
- Department of Experimental Oncology; IEO; European Institute of Oncology IRCCS; Milan Italy
| | - Giulio Pavesi
- Department of Biosciences; Università degli Studi di Milano; Milano 20133 Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology; IEO; European Institute of Oncology IRCCS; Milan Italy
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48
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Kalpage HA, Bazylianska V, Recanati MA, Fite A, Liu J, Wan J, Mantena N, Malek MH, Podgorski I, Heath EI, Vaishnav A, Edwards BF, Grossman LI, Sanderson TH, Lee I, Hüttemann M. Tissue-specific regulation of cytochrome c by post-translational modifications: respiration, the mitochondrial membrane potential, ROS, and apoptosis. FASEB J 2019; 33:1540-1553. [PMID: 30222078 PMCID: PMC6338631 DOI: 10.1096/fj.201801417r] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/14/2018] [Indexed: 02/02/2023]
Abstract
Cytochrome c (Cyt c) plays a vital role in the mitochondrial electron transport chain (ETC). In addition, it is a key regulator of apoptosis. Cyt c has multiple other functions including ROS production and scavenging, cardiolipin peroxidation, and mitochondrial protein import. Cyt c is tightly regulated by allosteric mechanisms, tissue-specific isoforms, and post-translational modifications (PTMs). Distinct residues of Cyt c are modified by PTMs, primarily phosphorylations, in a highly tissue-specific manner. These modifications downregulate mitochondrial ETC flux and adjust the mitochondrial membrane potential (ΔΨm), to minimize reactive oxygen species (ROS) production under normal conditions. In pathologic and acute stress conditions, such as ischemia-reperfusion, phosphorylations are lost, leading to maximum ETC flux, ΔΨm hyperpolarization, excessive ROS generation, and the release of Cyt c. It is also the dephosphorylated form of the protein that leads to maximum caspase activation. We discuss the complex regulation of Cyt c and propose that it is a central regulatory step of the mammalian ETC that can be rate limiting in normal conditions. This regulation is important because it maintains optimal intermediate ΔΨm, limiting ROS generation. We examine the role of Cyt c PTMs, including phosphorylation, acetylation, methylation, nitration, nitrosylation, and sulfoxidation and consider their potential biological significance by evaluating their stoichiometry.-Kalpage, H. A., Bazylianska, V., Recanati, M. A., Fite, A., Liu, J., Wan, J., Mantena, N., Malek, M. H., Podgorski, I., Heath, E. I., Vaishnav, A., Edwards, B. F., Grossman, L. I., Sanderson, T. H., Lee, I., Hüttemann, M. Tissue-specific regulation of cytochrome c by post-translational modifications: respiration, the mitochondrial membrane potential, ROS, and apoptosis.
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Affiliation(s)
- Hasini A. Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Viktoriia Bazylianska
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Maurice A. Recanati
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Alemu Fite
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Nikhil Mantena
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Moh H. Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Izabela Podgorski
- Department of Pharmacology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Elizabeth I. Heath
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Brian F. Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Thomas H. Sanderson
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Emergency Medicine, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do, South Korea
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
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Fulton MD, Brown T, Zheng YG. Mechanisms and Inhibitors of Histone Arginine Methylation. CHEM REC 2018; 18:1792-1807. [PMID: 30230223 PMCID: PMC6348102 DOI: 10.1002/tcr.201800082] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022]
Abstract
Histone methylation plays an important regulatory role in chromatin restructuring and RNA transcription. Arginine methylation that is enzymatically catalyzed by the family of protein arginine methyltransferases (PRMTs) can either activate or repress gene expression depending on cellular contexts. Given the strong correlation of PRMTs with pathophysiology, great interest is seen in understanding molecular mechanisms of PRMTs in diseases and in developing potent PRMT inhibitors. Herein, we reviewed key research advances in the study of biochemical mechanisms of PRMT catalysis and their relevance to cell biology. We highlighted how a random binary, ordered ternary kinetic model for PRMT1 catalysis reconciles the literature reports and endorses a distributive mechanism that the enzyme active site utilizes for multiple turnovers of arginine methylation. We discussed the impacts of histone arginine methylation and its biochemical interplays with other key epigenetic marks. Challenges in developing small-molecule PRMT inhibitors were also discussed.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA 30602
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA 30602
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, University of Georgia, Athens, GA 30602
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50
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Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci 2018; 5:90. [PMID: 30467545 PMCID: PMC6236024 DOI: 10.3389/fmolb.2018.00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
The interaction between non-coding RNAs (ncRNAs) and proteins is crucial for the stability, localization and function of the different classes of ncRNAs. Although ncRNAs, when embedded in various ribonucleoprotein (RNP) complexes, control the fundamental processes of gene expression, their biological functions and mechanisms of action are still largely unexplored. Mass Spectrometry (MS)-based proteomics has emerged as powerful tool to study the ncRNA world: on the one hand, by identifying the proteins interacting with distinct ncRNAs; on the other hand, by measuring the impact of ncRNAs on global protein levels. Here, we will first provide a concise overview on the basic principles of MS-based proteomics for systematic protein identification and quantification; then, we will recapitulate the main approaches that have been implemented for the screening of ncRNA interactors and the dissection of ncRNA-protein complex composition. Finally, we will describe examples of various proteomics strategies developed to characterize the effect of ncRNAs on gene expression, with a focus on the systematic identification of microRNA (miRNA) targets.
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Affiliation(s)
| | | | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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