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Wegman R, Langberg M, Davis RB, Liu X, Luo M, Yu MC, Walker SE. Protein Arginine Methylation of the Translation Initiation Factor eIF1A Increases Usage of a Near-cognate Start Codon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.608280. [PMID: 39185183 PMCID: PMC11343201 DOI: 10.1101/2024.08.16.608280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Protein arginine methylation has emerged as a key post-translational modification responsible for many facets of eukaryotic gene expression. To better understand the extent of this modification in cellular pathways, we carried out bioorthogonal methylation profiling in Saccharomyces cerevisiae to comprehensively identify the in vivo substrates of the major yeast protein arginine methyltransferase Hmt1. Gene ontology analysis of candidate substrates revealed an enrichment of proteins involved in the process of translation. We verified one such factor, eIF1A, by in vitro methylation. Three sites on eIF1A were found to be responsible for its methylation: R13, R14, and R62, with varied capacity by which each site contributed to the overall methylation capacity in vitro. To determine the role of methylation in eIF1A function, we used a battery of arginine-to-alanine substitution mutants to evaluate translation fidelity in these mutants. Our data show that substitution mutants at R13 and R14 in the N-terminal tail improved the fidelity of start codon recognition in an initiation fidelity assay. Overall, our data suggest that Hmt1-mediated methylation of eIF1A fine-tunes the fidelity of start codon recognition for proper translation initiation.
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Affiliation(s)
| | - Michael Langberg
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Richoo B. Davis
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, United States of America
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Xiaozhuo Liu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, United States of America
| | - Michael C. Yu
- Address correspondence to: M.L, M.C.Y., and S.E.W., Minkui Luo, Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY. 10065, Fax: 646-888-3166, ; Sarah E. Walker, Department of Biological Sciences, State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY. 14260, Fax: 716-645-2975, ; Michael C. Yu, Department of Biological Sciences, State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY. 14260, Fax: 716-645-2975,
| | - Sarah E. Walker
- Address correspondence to: M.L, M.C.Y., and S.E.W., Minkui Luo, Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY. 10065, Fax: 646-888-3166, ; Sarah E. Walker, Department of Biological Sciences, State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY. 14260, Fax: 716-645-2975, ; Michael C. Yu, Department of Biological Sciences, State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY. 14260, Fax: 716-645-2975,
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2
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Watanabe T, Kimura Y, Umeno D. Systematic promoter design for plasmid-encoded S-adenosylmethionine sensing systems. J GEN APPL MICROBIOL 2024; 70:n/a. [PMID: 38281753 DOI: 10.2323/jgam.2024.01.002] [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] [Indexed: 01/30/2024]
Abstract
S-adenosylmethionine (SAM) is an important biomolecule that mainly acts as a methyl donor and plays many roles in a variety of biological functions. SAM is also required for the biosynthesis of valuable methylated compounds, but its supply is a bottleneck for these biosynthetic pathways. To overcome this bottleneck and to reconfigure SAM homeostasis, a high-throughput sensing system for changes in intracellular SAM availability is required. We constructed a plasmid that can detect the factors that can alter SAM availability using minimal components. It does so by placing a fluorescent protein under a promoter controlled by endogenous MetJ, a transcription factor that represses its own regulons upon binding with SAM. Next, to validate SAM-responsive behavior, we systematically reconstructed 10 synthetic promoters with different positions and with different number of metbox sites. We found that a position between the -35 box and the -10 box was the most effective for repression and that this setup was suitable for detecting the genetic or environmental factors that can deplete and recover the intracellular SAM availability. Overall, the response patterns of the synthetic MetJ-regulated promoters characterized in this study may be useful for the development of better SAM biosensing systems.
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Affiliation(s)
- Taro Watanabe
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
- Kirin Central Research Institute, Kirin Holdings Company, Limited
| | - Yuki Kimura
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
| | - Daisuke Umeno
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
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3
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Zhang Y, Xu W, Peng C, Ren S, Zhang C. Intricate effects of post-translational modifications in liver cancer: mechanisms to clinical applications. J Transl Med 2024; 22:651. [PMID: 38997696 PMCID: PMC11245821 DOI: 10.1186/s12967-024-05455-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024] Open
Abstract
Liver cancer is a significant global health challenge, with hepatocellular carcinoma (HCC) being the most prevalent form, characterized by high incidence and mortality rates. Despite advances in targeted therapies and immunotherapies, the prognosis for advanced liver cancer remains poor. This underscores the urgent need for a deeper understanding of the molecular mechanisms underlying HCC to enable early detection and the development of novel therapeutic strategies. Post-translational modifications (PTMs) are crucial regulatory mechanisms in cellular biology, affecting protein functionality, interactions, and localization. These modifications, including phosphorylation, acetylation, methylation, ubiquitination, and glycosylation, occur after protein synthesis and play vital roles in various cellular processes. Recent advances in proteomics and molecular biology have highlighted the complex networks of PTMs, emphasizing their critical role in maintaining cellular homeostasis and disease pathogenesis. Dysregulation of PTMs has been associated with several malignant cellular processes in HCC, such as altered cell proliferation, migration, immune evasion, and metabolic reprogramming, contributing to tumor growth and metastasis. This review aims to provide a comprehensive understanding of the pathological mechanisms and clinical implications of various PTMs in liver cancer. By exploring the multifaceted interactions of PTMs and their impact on liver cancer progression, we highlight the potential of PTMs as biomarkers and therapeutic targets. The significance of this review lies in its potential to inform the development of novel therapeutic approaches and improve prognostic tools for early intervention in the fight against liver cancer.
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Affiliation(s)
- Yu Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weihao Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chuanhui Peng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shenli Ren
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Cheng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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4
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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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5
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Gao ST, Xin X, Wang ZY, Hu YY, Feng Q. USP5: Comprehensive insights into structure, function, biological and disease-related implications, and emerging therapeutic opportunities. Mol Cell Probes 2024; 73:101944. [PMID: 38049041 DOI: 10.1016/j.mcp.2023.101944] [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: 07/27/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023]
Abstract
Ubiquitin specific protease 5 (USP5) is a vital deubiquitinating enzyme that regulates various physiological functions by removing ubiquitin chains from target proteins. This review provides an overview of the structural and functional characteristics of USP5. Additionally, we discuss the role of USP5 in regulating diverse cellular processes, including cell proliferation, apoptosis, DNA double-strand damage, methylation, heat stress, and protein quality control, by targeting different substrates. Furthermore, we describe the involvement of USP5 in several pathological conditions such as tumors, pathological pain, developmental abnormalities, inflammatory diseases, and virus infection. Finally, we introduce newly developed inhibitors of USP5. In conclusion, investigating the novel functions and substrates of USP5, elucidating the underlying mechanisms of USP5-substrate interactions, intensifying the development of inhibitors, and exploring the upstream regulatory mechanisms of USP5 in detail can provide a new theoretical basis for the treatment of various diseases, including cancer, which is a promising research direction with considerable potential. Overall, USP5 plays a critical role in regulating various physiological and pathological processes, and investigating its novel functions and regulatory mechanisms may have significant implications for the development of therapeutic strategies for cancer and other diseases.
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Affiliation(s)
- Si-Ting Gao
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Xin
- Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China
| | - Zhuo-Yuan Wang
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi-Yang Hu
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China; Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China.
| | - Qin Feng
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China; Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China.
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6
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Ni J, Li S, Lai Y, Wang Z, Wang D, Tan Y, Fan Y, Lu J, Yao YF. Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function. Nucleic Acids Res 2023; 51:10411-10427. [PMID: 37742082 PMCID: PMC10602876 DOI: 10.1093/nar/gkad768] [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: 04/26/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Acetylation is a global post-translational modification that regulates various cellular processes. Bacterial acetylomic studies have revealed extensive acetylation of ribosomal proteins. However, the role of acetylation in regulating ribosome function remains poorly understood. In this study, we systematically profiled ribosomal protein acetylation and identified a total of 289 acetylated lysine residues in 52 ribosomal proteins (r-proteins) from Salmonella Typhimurium. The majority of acetylated lysine residues of r-proteins were found to be regulated by both acetyltransferase Pat and metabolic intermediate acetyl phosphate. Our results show that acetylation plays a critical role in the assembly of the mature 70S ribosome complex by modulating r-proteins binding to rRNA. Moreover, appropriate acetylation is important for the interactions between elongation factors and polysomes, as well as regulating ribosome translation efficiency and fidelity. Dysregulation of acetylation could alter bacterial sensitivity to ribosome-targeting antibiotics. Collectively, our data suggest that the acetylation homeostasis of ribosomes is crucial for their assembly and function. Furthermore, this mechanism may represent a universal response to environmental signals across different cell types.
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Affiliation(s)
- Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shuxian Li
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanan Lai
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongcong Tan
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongqiang Fan
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
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7
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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8
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Remines M, Schoonover M, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544294. [PMID: 37333147 PMCID: PMC10274911 DOI: 10.1101/2023.06.09.544294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in S. cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components, equal to 1440 wells, and measured for growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. In this study, we explore how the phenotypic growth differences are linked to the altered gene expression, and thereby predict the mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact S. cerevisiae pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart, even when the conditions tested were not specifically selected as targeting known methyl involving pathways. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role is production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Makailyn Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kellyn M. Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Erin D. Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
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9
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Karipal Padinjare Veedu D, Connal LA, Malins LR. Tunable Electrochemical Peptide Modifications: Unlocking New Levels of Orthogonality for Side-Chain Functionalization. Angew Chem Int Ed Engl 2023; 62:e202215470. [PMID: 36336657 PMCID: PMC10107541 DOI: 10.1002/anie.202215470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Electrochemical transformations provide enticing opportunities for programmable, residue-specific peptide modifications. Herein, we harness the potential of amidic side-chains as underutilized handles for late-stage modification through the development of an electroauxiliary-assisted oxidation of glutamine residues within unprotected peptides. Glutamine building blocks bearing electroactive side-chain N,S-acetals are incorporated into peptides using standard Fmoc-SPPS. Anodic oxidation of the electroauxiliary in the presence of diverse alcohol nucleophiles enables the installation of high-value N,O-acetal functionalities. Proof-of-principle for an electrochemical peptide stapling protocol, as well as the functionalization of dynorphin B, an endogenous opioid peptide, demonstrates the applicability of the method to intricate peptide systems. Finally, the site-selective and tunable electrochemical modification of a peptide bearing two discretely oxidizable sites is achieved.
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Affiliation(s)
- Dhanya Karipal Padinjare Veedu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A Connal
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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10
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Hapke R, Venton L, Rose KL, Sheng Q, Reddy A, Prather R, Jones A, Rathmell WK, Haake SM. SETD2 regulates the methylation of translation elongation factor eEF1A1 in clear cell renal cell carcinoma. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2022; 6:179-193. [PMID: 36684483 PMCID: PMC9851421 DOI: 10.3233/kca-220009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND SET domain-containing protein 2 (SETD2) is commonly mutated in renal cell carcinoma. SETD2 methylates histone H3 as well as a growing list of non-histone proteins. OBJECTIVE Initially, we sought to explore SETD2-dependent changes in lysine methylation of proteins in proximal renal tubule cells. Subsequently, we focused on changes in lysine methylation of the translation elongation factor eEF1A1. METHODS To accomplish these objectives, we initially performed a systems-wide analysis of protein lysine-methylation and expression in wild type (WT) and SETD2-knock out (KO) kidney cells and later focused our studies on eEF1A1 as well as the expression of lysine methyltransferases that regulate its lysine methylation. RESULTS We observed decreased lysine methylation of the translation elongation factor eEF1A1. EEF1AKMT2 and EEF1AKMT3 are known to methylate eEF1A1, and we show here that their expression is dependent on SET-domain function of SETD2. Globally, we observe differential expression of hundreds of proteins in WT versus SETD2-KO cells, including increased expression of many involved in protein translation. Finally, we observe decreased progression free survival and loss of EEF1AKMT2 gene expression in SETD2-mutated tumors predicted to have loss of function of the SET domain. CONCLUSION Overall, these data suggest that SETD2-mutated ccRCC, via loss of enzymatic function of the SET domain, displays dysregulation of protein translation as a potentially important component of the transformed phenotype.
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Affiliation(s)
- Robert Hapke
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Venton
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristie Lindsay Rose
- Mass Spectrometry Research Center, Proteomics Core Laboratory, Vanderbilt University, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Rebecca Prather
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Angela Jones
- Vanderbilt Technologies for Advanced Genomics (VANTAGE), Vanderbilt University Medical Center, Nashville, TN, USA
| | - W. Kimryn Rathmell
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott M. Haake
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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11
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Biziaev NS, Shuvalov AV, Alkalaeva EZ. HEMK-Like Methyltransferases in the Regulation of Cellular Processes. Mol Biol 2022. [DOI: 10.1134/s0026893322030025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Alam M, Shima H, Matsuo Y, Long NC, Matsumoto M, Ishii Y, Sato N, Sugiyama T, Nobuta R, Hashimoto S, Liu L, Kaneko MK, Kato Y, Inada T, Igarashi K. mTORC1-independent translation control in mammalian cells by methionine adenosyltransferase 2A and S-adenosylmethionine. J Biol Chem 2022; 298:102084. [PMID: 35636512 PMCID: PMC9243181 DOI: 10.1016/j.jbc.2022.102084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM). As the sole methyl-donor for methylation of DNA, RNA, and proteins, SAM levels affect gene expression by changing methylation patterns. Expression of MAT2A, the catalytic subunit of isozyme MAT2, is positively correlated with proliferation of cancer cells; however, how MAT2A promotes cell proliferation is largely unknown. Given that the protein synthesis is induced in proliferating cells and that RNA and protein components of translation machinery are methylated, we tested here whether MAT2 and SAM are coupled with protein synthesis. By measuring ongoing protein translation via puromycin labeling, we revealed that MAT2A depletion or chemical inhibition reduced protein synthesis in HeLa and Hepa1 cells. Furthermore, overexpression of MAT2A enhanced protein synthesis, indicating that SAM is limiting under normal culture conditions. In addition, MAT2 inhibition did not accompany reduction in mechanistic target of rapamycin complex 1 activity but nevertheless reduced polysome formation. Polysome-bound RNA sequencing revealed that MAT2 inhibition decreased translation efficiency of some fraction of mRNAs. MAT2A was also found to interact with the proteins involved in rRNA processing and ribosome biogenesis; depletion or inhibition of MAT2 reduced 18S rRNA processing. Finally, quantitative mass spectrometry revealed that some translation factors were dynamically methylated in response to the activity of MAT2A. These observations suggest that cells possess an mTOR-independent regulatory mechanism that tunes translation in response to the levels of SAM. Such a system may acclimate cells for survival when SAM synthesis is reduced, whereas it may support proliferation when SAM is sufficient.
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Affiliation(s)
- Mahabub Alam
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Animal Science and Nutrition, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Matsuo
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nguyen Chi Long
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yusho Ishii
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nichika Sato
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takato Sugiyama
- Laboratory of Gene Regulation, Department of Molecular Biopharmacy and Genetics, Tohoku University Graduate School of Pharmaceutical Science, Sendai, Japan
| | - Risa Nobuta
- Laboratory of Gene Regulation, Department of Molecular Biopharmacy and Genetics, Tohoku University Graduate School of Pharmaceutical Science, Sendai, Japan
| | - Satoshi Hashimoto
- Laboratory of Gene Regulation, Department of Molecular Biopharmacy and Genetics, Tohoku University Graduate School of Pharmaceutical Science, Sendai, Japan
| | - Liang Liu
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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13
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Shrestha HK, Appidi MR, Villalobos Solis MI, Wang J, Carper DL, Burdick L, Pelletier DA, Doktycz MJ, Hettich RL, Abraham PE. Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance. BMC Microbiol 2021; 21:308. [PMID: 34749649 PMCID: PMC8574000 DOI: 10.1186/s12866-021-02370-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02370-4.
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Affiliation(s)
- Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.,Department of Genome Science and Technology, University of Tennessee-Knoxville, 37996, Knoxville, Tennessee, United States
| | - Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.,Department of Genome Science and Technology, University of Tennessee-Knoxville, 37996, Knoxville, Tennessee, United States
| | | | - Jia Wang
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Leah Burdick
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.
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14
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Parada C, Neri-Badillo IC, Vallecillo AJ, Segura E, Silva-Miranda M, Guzmán-Gutiérrez SL, Ortega PA, Coronado-Aceves EW, Cancino-Villeda L, Torres-Larios A, Aceves Sánchez MDJ, Flores Valdez MA, Espitia C. New Insights into the Methylation of Mycobacterium tuberculosis Heparin Binding Hemagglutinin Adhesin Expressed in Rhodococcus erythropolis. Pathogens 2021; 10:pathogens10091139. [PMID: 34578171 PMCID: PMC8467707 DOI: 10.3390/pathogens10091139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
In recent years, knowledge of the role that protein methylation is playing on the physiopathogenesis of bacteria has grown. In Mycobacterium tuberculosis, methylation of the heparin binding hemagglutinin adhesin modulates the immune response, making this protein a subunit vaccine candidate. Through its C-terminal lysine-rich domain, this surface antigen interacts with heparan sulfate proteoglycans present in non-phagocytic cells, leading to extrapulmonary dissemination of the pathogen. In this study, the adhesin was expressed as a recombinant methylated protein in Rhodococcus erythropolis L88 and it was found associated to lipid droplets when bacteria were grown under nitrogen limitation. In order to delve into the role methylation could have in host–pathogen interactions, a comparative analysis was carried out between methylated and unmethylated protein produced in Escherichia coli. We found that methylation had an impact on lowering protein isoelectric point, but no differences between the proteins were found in their capacity to interact with heparin and A549 epithelial cells. An important finding was that HbhA is a Fatty Acid Binding Protein and differences in the conformational stability of the protein in complex with the fatty acid were observed between methylated and unmethylated protein. Together, these results suggest that the described role for this mycobacteria protein in lipid bodies formation could be related to its capacity to transport fatty acids. Obtained results also provide new clues about the role HbhA methylation could have in tuberculosis and point out the importance of having heterologous expression systems to obtain modified proteins.
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Affiliation(s)
- Cristina Parada
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Isabel Cecilia Neri-Badillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Antonio J. Vallecillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Facultad de Ciencias Agropecuarias, Universidad de Cuenca, Cuenca 010220, Ecuador
| | - Erika Segura
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Mayra Silva-Miranda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Silvia Laura Guzmán-Gutiérrez
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Paola A. Ortega
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Enrique Wenceslao Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Laura Cancino-Villeda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Alfredo Torres-Larios
- Department of Biochemistry and Structural Biology, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Michel de Jesús Aceves Sánchez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Mario Alberto Flores Valdez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Correspondence:
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15
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Wei HH, Fan XJ, Hu Y, Tian XX, Guo M, Mao MW, Fang ZY, Wu P, Gao SX, Peng C, Yang Y, Wang Z. A systematic survey of PRMT interactomes reveals the key roles of arginine methylation in the global control of RNA splicing and translation. Sci Bull (Beijing) 2021; 66:1342-1357. [PMID: 36654156 DOI: 10.1016/j.scib.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/13/2020] [Accepted: 12/30/2020] [Indexed: 01/20/2023]
Abstract
Thousands of proteins undergo arginine methylation, a widespread post-translational modification catalyzed by several protein arginine methyltransferases (PRMTs). However, global understanding of their biological functions is limited due to the lack of a complete picture of the catalytic network for each PRMT. Here, we systematically identified interacting proteins for all human PRMTs and demonstrated their functional importance in mRNA splicing and translation. We demonstrated significant overlapping of interactomes of human PRMTs with the known methylarginine-containing proteins. Different PRMTs are functionally redundant with a high degree of overlap in their substrates and high similarities between their putative methylation motifs. Importantly, RNA-binding proteins involved in regulating RNA splicing and translation contain highly enriched arginine methylation regions. Moreover, inhibition of PRMTs globally alternates alternative splicing (AS) and suppresses translation. In particular, ribosomal proteins are extensively modified with methylarginine, and mutations in their methylation sites suppress ribosome assembly, translation, and eventually cell growth. Collectively, our study provides a global view of different PRMT networks and uncovers critical functions of arginine methylation in regulating mRNA splicing and translation.
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Affiliation(s)
- Huan-Huan Wei
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xiao-Juan Fan
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Hu
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Xu Tian
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Meng Guo
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710000, China
| | - Miao-Wei Mao
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhao-Yuan Fang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Shuai-Xin Gao
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhang-Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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16
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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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17
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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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18
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Shetty S, Varshney U. Regulation of translation by one-carbon metabolism in bacteria and eukaryotic organelles. J Biol Chem 2021; 296:100088. [PMID: 33199376 PMCID: PMC7949028 DOI: 10.1074/jbc.rev120.011985] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Protein synthesis is an energetically costly cellular activity. It is therefore important that the process of mRNA translation remains in excellent synchrony with cellular metabolism and its energy reserves. Unregulated translation could lead to the production of incomplete, mistranslated, or misfolded proteins, squandering the energy needed for cellular sustenance and causing cytotoxicity. One-carbon metabolism (OCM), an integral part of cellular intermediary metabolism, produces a number of one-carbon unit intermediates (formyl, methylene, methenyl, methyl). These OCM intermediates are required for the production of amino acids such as methionine and other biomolecules such as purines, thymidylate, and redox regulators. In this review, we discuss how OCM impacts the translation apparatus (composed of ribosome, tRNA, mRNA, and translation factors) and regulates crucial steps in protein synthesis. More specifically, we address how the OCM metabolites regulate the fidelity and rate of translation initiation in bacteria and eukaryotic organelles such as mitochondria. Modulation of the fidelity of translation initiation by OCM opens new avenues to understand alternative translation mechanisms involved in stress tolerance and drug resistance.
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Affiliation(s)
- Sunil Shetty
- Biozentrum, University of Basel, Basel, Switzerland
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India; Jawaharlal Nehru Centre for Advanced Scientific Studies, Jakkur, Bangalore, India.
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19
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Lacoux C, Wacheul L, Saraf K, Pythoud N, Huvelle E, Figaro S, Graille M, Carapito C, Lafontaine DLJ, Heurgué-Hamard V. The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis. Nucleic Acids Res 2020; 48:12310-12325. [PMID: 33166396 PMCID: PMC7708063 DOI: 10.1093/nar/gkaa972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/14/2023] Open
Abstract
The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination.
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Affiliation(s)
- Caroline Lacoux
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Kritika Saraf
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), UMR 7178, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Emmeline Huvelle
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sabine Figaro
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), UMR 7178, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Valérie Heurgué-Hamard
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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20
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Takahashi-Nakaguchi A, Shishido E, Yahara M, Urayama SI, Ninomiya A, Chiba Y, Sakai K, Hagiwara D, Chibana H, Moriyama H, Gonoi T. Phenotypic and Molecular Biological Analysis of Polymycovirus AfuPmV-1M From Aspergillus fumigatus: Reduced Fungal Virulence in a Mouse Infection Model. Front Microbiol 2020; 11:607795. [PMID: 33424809 PMCID: PMC7794001 DOI: 10.3389/fmicb.2020.607795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/24/2020] [Indexed: 11/30/2022] Open
Abstract
The filamentous fungal pathogen Aspergillus fumigatus is one of the most common causal agents of invasive fungal infection in humans; the infection is associated with an alarmingly high mortality rate. In this study, we investigated whether a mycovirus, named AfuPmV-1M, can reduce the virulence of A. fumigatus in a mouse infection model. AfuPmV-1M has high sequence similarity to AfuPmV-1, one of the polymycovirus that is a capsidless four-segment double-stranded RNA (dsRNA) virus, previously isolated from the genome reference strain of A. fumigatus, Af293. However, we found the isolate had an additional fifth dsRNA segment, referred to as open reading frame 5 (ORF5), which has not been reported in AfuPmV-1. We then established isogenic lines of virus-infected and virus-free A. fumigatus strains. Mycovirus infection had apparent influences on fungal phenotypes, with the virus-infected strain producing a reduced mycelial mass and reduced conidial number in comparison with these features of the virus-free strain. Also, resting conidia of the infected strain showed reduced adherence to pulmonary epithelial cells and reduced tolerance to macrophage phagocytosis. In an immunosuppressed mouse infection model, the virus-infected strain showed reduced mortality in comparison with mortality due to the virus-free strain. RNA sequencing and high-performance liquid chromatography (HPLC) analysis showed that the virus suppressed the expression of genes for gliotoxin synthesis and its production at the mycelial stage. Conversely, the virus enhanced gene expression and biosynthesis of fumagillin. Viral RNA expression was enhanced during conidial maturation, conidial germination, and the mycelial stage. We presume that the RNA or translation products of the virus affected fungal phenotypes, including spore formation and toxin synthesis. To identify the mycovirus genes responsible for attenuation of fungal virulence, each viral ORF was ectopically expressed in the virus-free KU strain. We found that the expression of ORF2 and ORF5 reduced fungal virulence in the mouse model. In addition, ORF3 affected the stress tolerance of host A. fumigatus in culture. We hypothesize that the respective viral genes work cooperatively to suppress the pathogenicity of the fungal host.
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Affiliation(s)
| | - Erika Shishido
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Misa Yahara
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Syun-Ichi Urayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Akihiro Ninomiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuto Chiba
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kanae Sakai
- Medical Mycology Research Center, Chiba University, Chiba, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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21
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Lomakin IB, De S, Wang J, Borkar AN, Steitz TA. Crystal structure of the C-terminal domain of DENR. Comput Struct Biotechnol J 2020; 18:696-704. [PMID: 32257053 PMCID: PMC7114459 DOI: 10.1016/j.csbj.2020.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023] Open
Abstract
The density regulated protein (DENR) forms a stable heterodimer with malignant T-cell-amplified sequence 1 (MCT-1). DENR-MCT-1 heterodimer then participates in regulation of non-canonical translation initiation and ribosomal recycling. The N-terminal domain of DENR interacts with MCT-1 and carries a classical tetrahedral zinc ion-binding site, which is crucial for the dimerization. DENR-MCT-1 binds the small (40S) ribosomal subunit through interactions between MCT-1 and helix h24 of the 18S rRNA, and through interactions between the C-terminal domain of DENR and helix h44 of the 18S rRNA. This later interaction occurs in the vicinity of the P site that is also the binding site for canonical translation initiation factor eIF1, which plays the key role in initiation codon selection and scanning. Sequence homology modeling and a low-resolution crystal structure of the DENR-MCT-1 complex with the human 40S subunit suggests that the C-terminal domain of DENR and eIF1 adopt a similar fold. Here we present the crystal structure of the C-terminal domain of DENR determined at 1.74 Å resolution, which confirms its resemblance to eIF1 and advances our understanding of the mechanism by which DENR-MCT-1 regulates non-canonical translation initiation and ribosomal recycling.
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Affiliation(s)
- Ivan B. Lomakin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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22
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White JT, Cato T, Deramchi N, Gabunilas J, Roy KR, Wang C, Chanfreau GF, Clarke SG. Protein Methylation and Translation: Role of Lysine Modification on the Function of Yeast Elongation Factor 1A. Biochemistry 2019; 58:4997-5010. [PMID: 31738538 DOI: 10.1021/acs.biochem.9b00818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1-7 and Rkm 1-5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 and Efm4-7) appear to be specific to elongation factor 1A (EF1A), the protein responsible for bringing aminoacyl-tRNAs to the ribosome. In S. cerevisiae, the functional implications of lysine methylation in translation are mostly unknown. In this work, we assessed the physiological impact of disrupting EF1A methylation in a strain where four of the most conserved methylated lysine sites are mutated to arginine residues and in strains lacking either four or five of the Efm lysine methyltransferases specific to EF1A. We found that loss of EF1A methylation was not lethal but resulted in reduced growth rates, particularly under caffeine and rapamycin stress conditions, suggesting EF1A interacts with the TORC1 pathway, as well as altered sensitivities to ribosomal inhibitors. We also detected reduced cellular levels of the EF1A protein, which surprisingly was not reflected in its stability in vivo. We present evidence that these Efm methyltransferases appear to be largely devoted to the modification of EF1A, finding no evidence of the methylation of other substrates in the yeast cell. This work starts to illuminate why one protein can need five different methyltransferases for its functions and highlights the resilience of yeast to alterations in their posttranslational modifications.
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Affiliation(s)
- Jonelle T White
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Tieranee Cato
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Neil Deramchi
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Kevin R Roy
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Charles Wang
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
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23
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Ishiguro K, Arai T, Suzuki T. Depletion of S-adenosylmethionine impacts on ribosome biogenesis through hypomodification of a single rRNA methylation. Nucleic Acids Res 2019; 47:4226-4239. [PMID: 30799486 PMCID: PMC6486555 DOI: 10.1093/nar/gkz111] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 11/14/2022] Open
Abstract
S-adenosylmethionine (SAM) is an essential metabolite and a methyl group donor in all living organisms. The intracellular SAM concentration is tightly regulated, and depletion causes hypomethylation of substrates, growth defects and pathological consequences. In the emerging field of epitranscriptomics, SAM-dependent RNA methylations play a critical role in gene expression. Herein, we analyzed the methylation status of ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) in Escherichia coli Δmtn strain in which cellular SAM was down-regulated, and found hypomodification of several methylation sites, including 2′-O-methylation at position 2552 (Um2552) of 23S rRNA. We observed severe growth defect of the Δmtn strain with significant accumulation of 45S ribosomal precursor harboring 23S rRNA with hypomodified Um2552. Strikingly, the growth defect was partially restored by overexpression of rlmE encoding the SAM-dependent methyltransferase responsible for Um2552. Although SAM is involved not only in rRNA methylation but also in various cellular processes, effects on ribosome biogenesis contribute substantially to the observed defects on cell proliferation.
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Affiliation(s)
- Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taiga Arai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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24
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Vedarethinam V, Huang L, Xu W, Zhang R, Gurav DD, Sun X, Yang J, Chen R, Qian K. Detection and Inhibition of Bacteria on a Dual-Functional Silver Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1803051. [PMID: 30358085 DOI: 10.1002/smll.201803051] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/08/2018] [Indexed: 05/24/2023]
Abstract
Detection and inhibition of bacteria are universally required in clinics and daily life for health care. Developing a dual-functional material is challenging and in demand, engaging advanced applications for both defined bioanalysis and targeted biotoxicity. Herein, magnetic silver nanoshells are designed as a multifunctional platform for the detection and inhibition of bacteria. The optimized magnetic silver nanoshells enable direct laser desorption/ionization mass spectrometry based metabolic analysis of bacteria (≈10 µL-1 ), in complex biofluids. The serum infection process (0-10 h) is monitored by statistics toward clinical classification. Moreover, magnetic silver nanoshells facilitate surface adhesion on bacteria due to nanoscale surface roughness and thus display long-term antibacterial effects. Bacteria metabolism is studied with metabolic biomarkers (e.g., malate and lysine) identified during inhibition, showing cell membrane destruction and dysfunctional protein synthesis mechanisms. This work not only guides the design of material-based approaches for bioanalysis and biotoxicity, but contributes to bacteria-related diagnosis by using specific metabolic biomarkers for sensitive detection and new insights by monitoring metabolomic change of bacteria for antibacterial applications.
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Affiliation(s)
- Vadanasundari Vedarethinam
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Lin Huang
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wei Xu
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ru Zhang
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Deepanjali D Gurav
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xuming Sun
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jing Yang
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ruoping Chen
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
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25
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Obata F, Tsuda-Sakurai K, Yamazaki T, Nishio R, Nishimura K, Kimura M, Funakoshi M, Miura M. Nutritional Control of Stem Cell Division through S-Adenosylmethionine in Drosophila Intestine. Dev Cell 2018; 44:741-751.e3. [PMID: 29587144 DOI: 10.1016/j.devcel.2018.02.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 12/26/2017] [Accepted: 02/21/2018] [Indexed: 02/01/2023]
Abstract
The intestine has direct contact with nutritional information. The mechanisms by which particular dietary molecules affect intestinal homeostasis are not fully understood. In this study, we identified S-adenosylmethionine (SAM), a universal methyl donor synthesized from dietary methionine, as a critical molecule that regulates stem cell division in Drosophila midgut. Depletion of either dietary methionine or SAM synthesis reduces division rate of intestinal stem cells. Genetic screening for putative SAM-dependent methyltransferases has identified protein synthesis as a regulator of the stem cells, partially through a unique diphthamide modification on eukaryotic elongation factor 2. In contrast, SAM in nutrient-absorptive enterocytes controls the interleukin-6-like protein Unpaired 3, which is required for rapid division of the stem cells after refeeding. Our study sheds light upon a link between diet and intestinal homeostasis and highlights the key metabolite SAM as a mediator of cell-type-specific starvation response.
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Affiliation(s)
- Fumiaki Obata
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kayoko Tsuda-Sakurai
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Yamazaki
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Nishio
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kei Nishimura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaki Kimura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masabumi Funakoshi
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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26
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Clarke SG. The ribosome: A hot spot for the identification of new types of protein methyltransferases. J Biol Chem 2018; 293:10438-10446. [PMID: 29743234 DOI: 10.1074/jbc.aw118.003235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cellular physiology depends on the alteration of protein structures by covalent modification reactions. Using a combination of bioinformatic, genetic, biochemical, and mass spectrometric approaches, it has been possible to probe ribosomal proteins from the yeast Saccharomyces cerevisiae for post-translationally methylated amino acid residues and for the enzymes that catalyze these modifications. These efforts have resulted in the identification and characterization of the first protein histidine methyltransferase, the first N-terminal protein methyltransferase, two unusual types of protein arginine methyltransferases, and a new type of cysteine methylation. Two of these enzymes may modify their substrates during ribosomal assembly because the final methylated histidine and arginine residues are buried deep within the ribosome with contacts only with RNA. Two of these modifications occur broadly in eukaryotes, including humans, whereas the others demonstrate a more limited phylogenetic range. Analysis of strains where the methyltransferase genes are deleted has given insight into the physiological roles of these modifications. These reactions described here add diversity to the modifications that generate the typical methylated lysine and arginine residues previously described in histones and other proteins.
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Affiliation(s)
- Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095
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27
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Liu S, Yu F, Yang Z, Wang T, Xiong H, Chang C, Yu W, Li N. Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis. Mol Cell Proteomics 2018; 17:1010-1027. [PMID: 29440448 DOI: 10.1074/mcp.ra117.000530] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/18/2018] [Indexed: 12/19/2022] Open
Abstract
Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both CsCl density gradient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl chemical labeling with chromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based computational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named Stable isotope-based Quantitation-Dimethyl labeling (SQUA-D), and finally the confirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain (i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and 31 hormone-suppressed acetylpeptide groups or called unique PTM peptide arrays (UPAs) that share the identical unique PTM site pattern (UPSP). This CDG centrifugation protein fractionation in combination with dimethyl labeling-based quantitative PTM proteomics, and SQUA-D may be applied in the quantitation of any PTM proteins in any model eukaryotes and agricultural crops as well as tissue samples of animals and human beings.
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Affiliation(s)
- Shichang Liu
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Zhu Yang
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Tingliang Wang
- **Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hairong Xiong
- ‡‡College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Caren Chang
- §§Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland 20742-5815
| | - Weichuan Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
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28
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Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. J Proteome Res 2017; 17:568-578. [PMID: 29195273 DOI: 10.1021/acs.jproteome.7b00685] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes. It is applied here to reveal systemic proteoform variations in the yeast response to salt stress.
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Affiliation(s)
- Anthony J Cesnik
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Leah V Schaffer
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Rachel A Knoener
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Brian L Frey
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Stefan K Solntsev
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Yunxiang Dai
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Audrey P Gasch
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, ‡Laboratory of Genetics, and §Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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29
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Wang C, Wang Q, Xu X, Xie B, Zhao Y, Li N, Cao X. The methyltransferase NSD3 promotes antiviral innate immunity via direct lysine methylation of IRF3. J Exp Med 2017; 214:3597-3610. [PMID: 29101251 PMCID: PMC5716042 DOI: 10.1084/jem.20170856] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/18/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
Wang et al. demonstrate that methyltransferase NSD3 directly methylates IRF3 and maintains IRF3 phosphorylation to enhance its transcriptional activity by disassociating the methylated IRF3 and PP1cc to prevent IRF3 dephosphorylation, consequently promoting antiviral innate immune response. Lysine methylation is an important posttranslational modification, implicated in various biological pathological conditions. The transcription factor interferon regulatory factor 3 (IRF3) is essential for antiviral innate immunity, yet the mechanism for methylation control of IRF3 activation remains unclear. In this paper, we discovered monomethylation of IRF3 at K366 is critical for IRF3 transcription activity in antiviral innate immunity. By mass spectrometry analysis of IRF3-associated proteins, we identified nuclear receptor–binding SET domain 3 (NSD3) as the lysine methyltransferase that directly binds to the IRF3 C-terminal region through its PWWP1 domain and methylates IRF3 at K366 via its SET domain. Deficiency of NSD3 impairs the antiviral innate immune response in vivo. Mechanistically, NSD3 enhances the transcription activity of IRF3 dependent on K366 monomethylation, which maintains IRF3 phosphorylation by promoting IRF3 dissociation of protein phosphatase PP1cc and consequently promotes type I interferon production. Our study reveals a critical role of NSD3-mediated IRF3 methylation in enhancing antiviral innate immunity.
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Affiliation(s)
- Chunmei Wang
- Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Qinlan Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Xu
- Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Xie
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nan Li
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Xuetao Cao
- Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China .,National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
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30
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Malecki J, Aileni VK, Ho AYY, Schwarz J, Moen A, Sørensen V, Nilges BS, Jakobsson ME, Leidel SA, Falnes PØ. The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A). Nucleic Acids Res 2017; 45:4370-4389. [PMID: 28108655 PMCID: PMC5416902 DOI: 10.1093/nar/gkx002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/02/2017] [Indexed: 12/25/2022] Open
Abstract
Lysine methylation is abundant on histone proteins, representing a dynamic regulator of chromatin state and gene activity, but is also frequent on many non-histone proteins, including eukaryotic elongation factor 1 alpha (eEF1A). However, the functional significance of eEF1A methylation remains obscure and it has remained unclear whether eEF1A methylation is dynamic and subject to active regulation. We here demonstrate, using a wide range of in vitro and in vivo approaches, that the previously uncharacterized human methyltransferase METTL21B specifically targets Lys-165 in eEF1A in an aminoacyl-tRNA- and GTP-dependent manner. Interestingly, METTL21B-mediated eEF1A methylation showed strong variation across different tissues and cell lines, and was induced by altering growth conditions or by treatment with certain ER-stress-inducing drugs, concomitant with an increase in METTL21B gene expression. Moreover, genetic ablation of METTL21B function in mammalian cells caused substantial alterations in mRNA translation, as measured by ribosomal profiling. A non-canonical function for eEF1A in organization of the cellular cytoskeleton has been reported, and interestingly, METTL21B accumulated in centrosomes, in addition to the expected cytosolic localization. In summary, the present study identifies METTL21B as the enzyme responsible for methylation of eEF1A on Lys-165 and shows that this modification is dynamic, inducible and likely of regulatory importance.
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Affiliation(s)
- Jedrzej Malecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Vinay Kumar Aileni
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Juliane Schwarz
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Vigdis Sørensen
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway
| | - Benedikt S Nilges
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Magnus E Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
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31
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Kim D, Yang KY, Kim HM, Kim TR, Kim NJ, Shin S, Kim SK. Site-dependent effects of methylation on the electronic spectra of jet-cooled methylated xanthine compounds. Phys Chem Chem Phys 2017; 19:22375-22384. [PMID: 28805861 DOI: 10.1039/c7cp03380j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We obtained the electronic spectra of various methylated xanthine compounds including caffeine in a supersonic jet by resonant two-photon ionization spectroscopy. The methyl group in the tested methylated xanthine compounds has a distinct, site-dependent effect on the electronic spectrum. Methylation at the N3 position causes a significant red shift of the ππ* state, whereas methylation at the N1 position has only minimal effects on the electronic spectrum. The notably broad spectra of theobromine and caffeine result from methyl substitution at the N7 position, which causes a large displacement between the potential energy surfaces of the S0 and S1 states, and a strong vibronic coupling. We also investigated the internal rotation of the methyl group and its effect on the electronic spectrum of the methylated xanthine compounds. We found that the barrier height for the torsional motion in the ground state is significantly affected by a carbonyl or methyl group that lies close to the methyl group of interest. In contrast, the torsional barrier in the excited state is governed by the hyperconjugation interaction in the lowest unoccupied molecular orbital. The agreement between the experimental and simulated spectra of torsional vibronic bands suggested that the low frequency torsional vibrations arising from the tunneling splitting and the coupling between the torsional and molecular motions give theobromine and theophylline the multiplet nature of their origin bands. This study provides a new level of understanding for the methyl substitution effects on the electronically excited states of xanthine compounds, which may very well be applicable to many other methyl substituted biomolecules including DNAs and proteins.
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Affiliation(s)
- Doory Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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Semi-Quantitative Mass Spectrometry in AML Cells Identifies New Non-Genomic Targets of the EZH2 Methyltransferase. Int J Mol Sci 2017; 18:ijms18071440. [PMID: 28678185 PMCID: PMC5535931 DOI: 10.3390/ijms18071440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/29/2022] Open
Abstract
Alterations to the gene encoding the EZH2 (KMT6A) methyltransferase, including both gain-of-function and loss-of-function, have been linked to a variety of haematological malignancies and solid tumours, suggesting a complex, context-dependent role of this methyltransferase. The successful implementation of molecularly targeted therapies against EZH2 requires a greater understanding of the potential mechanisms by which EZH2 contributes to cancer. One aspect of this effort is the mapping of EZH2 partner proteins and cellular targets. To this end we performed affinity-purification mass spectrometry in the FAB-M2 HL-60 acute myeloid leukaemia (AML) cell line before and after all-trans retinoic acid-induced differentiation. These studies identified new EZH2 interaction partners and potential non-histone substrates for EZH2-mediated methylation. Our results suggest that EZH2 is involved in the regulation of translation through interactions with a number of RNA binding proteins and by methylating key components of protein synthesis such as eEF1A1. Given that deregulated mRNA translation is a frequent feature of cancer and that eEF1A1 is highly expressed in many human tumours, these findings present new possibilities for the therapeutic targeting of EZH2 in AML.
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33
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Barroso M, Handy DE, Castro R. The Link Between Hyperhomocysteinemia and Hypomethylation. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2017. [DOI: 10.1177/2326409817698994] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Madalena Barroso
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Diane E. Handy
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rita Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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34
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Eustache S, Créchet JB, Bouceba T, Nakayama JI, Tanaka M, Suzuki M, Woisard A, Tuffery P, Baouz S, Hountondji C. A Functional Role for the Monomethylated Gln-51 and Lys-53 Residues of the 49GGQTK53 Motif of eL42 from Human 80S Ribosomes. Open Biochem J 2017; 11:8-26. [PMID: 28567122 PMCID: PMC5418926 DOI: 10.2174/1874091x01711010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/06/2017] [Accepted: 01/10/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND We have previously demonstrated that the eukaryote-specific ribosomal protein eL42 of the human 80S ribosome contains seven monomethylated residues, among which are the Gln-51 and Lys-53 residues contained in the 47GFGGQTK53 sequence conserved in all eukaryotic 80S ribosomes. This sequence contains the methylated and universally conserved GGQ motif common for all class-1 translation termination factors responsible for stop codon recognition and for triggering the hydrolysis of the P site-bound peptidyl-tRNA. We have also recently reported a model of ribosomal ternary eL42-tRNA-eRF1 complex where specific regions of all three macromolecules (the comparably flexible GGQ domains of eRF1 and eL42 and the CCA-arm of tRNA) are involved in interactions. METHOD Here, we have studied the interactions between recombinant eL42 and eRF1 proteins and the tRNA substrate by means of the Biacore assay, using the wild-type eL42 protein, the eL42-Δ(GGQTK) mutant (the eL42 protein whose GGQTK motif has been deleted), the single Q51E and K53Q mutants (eL42-Q51E and eL42-K53Q, respectively), as well as the double Q51A/K53A mutant (eL42-Q51A/K53A). RESULTS Our results show that the monomethylated Gln-51 and Lys-53 residues contained in the 47GFGGQTK53 sequence of eL42 and the monomethylated GGQ motif of eRF1 represents the sites of interaction between these two proteins through hydrophobic contacts between methyl groups. We also demonstrate that the interactions between eL42 and tRNA or 28S rRNA are characterized by strong binding affinities (KD values in the nanomolar or picomolar range, respectively) which argue for specific interactions. Strong interactions between eL42 and tRNA are likely to be responsible for the decrease in the poly(U)-dependent poly(Phe) synthesis activity of human 80S or E. coli 70S ribosomes in the presence of added human recombinant eL42. It is proposed that the decrease of the activity of the ribosome is caused by the sequestration of the substrate Phe-tRNAPhe by the added eL42 protein. CONCLUSION Interactions between the monomethylated Gln-51 and Lys-53 residues of the 49GGQTK53 motif of the human eL42 protein and the methylated GGQ motif of eRF1 are likely to play a functional role on translating human 80S ribosomes.
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Affiliation(s)
- Stéphanie Eustache
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
- Université Paris-Diderot, Sorbonne-Paris-Cité, INSERM-UMR-S973 and RPBS, Paris, France
| | | | - Tahar Bouceba
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine (IBPS) Plateforme d’interactions moléculaires, CNRS-FR3631; 7, Quai Saint Bernard, F-75252, Paris Cedex 05, France
| | - Jun-ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501 Japan
| | - Mayo Tanaka
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501 Japan
| | - Mieko Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501 Japan
| | - Anne Woisard
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
| | - Pierre Tuffery
- Université Paris-Diderot, Sorbonne-Paris-Cité, INSERM-UMR-S973 and RPBS, Paris, France
| | - Soria Baouz
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
| | - Codjo Hountondji
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
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35
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Bourgeois G, Létoquart J, van Tran N, Graille M. Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus. Biomolecules 2017; 7:biom7010007. [PMID: 28134793 PMCID: PMC5372719 DOI: 10.3390/biom7010007] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and substrate recognition, as well as their implications in human diseases. Moreover, as Trm112 orthologs are found in bacterial and archaeal genomes, the conservation of this Trm112 network beyond eukaryotic organisms is also discussed.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
| | - Juliette Létoquart
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
- De Duve Institute, Université Catholique de Louvain, avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Nhan van Tran
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
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36
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Wang Q, Wang K, Ye M. Strategies for large-scale analysis of non-histone protein methylation by LC-MS/MS. Analyst 2017; 142:3536-3548. [DOI: 10.1039/c7an00954b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein methylation is an important post-translational modification (PTM) that plays crucial roles in the regulation of diverse biological processes.
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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
| | - 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
| | - 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
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37
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Caslavka Zempel KE, Vashisht AA, Barshop WD, Wohlschlegel JA, Clarke SG. Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC. J Proteome Res 2016; 15:4436-4451. [PMID: 27696855 DOI: 10.1021/acs.jproteome.6b00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methylation is a common and abundant post-translational modification. High-throughput proteomic investigations have reported many methylation sites from complex mixtures of proteins. The lack of consistency between parallel studies, resulting from both false positives and missed identifications, suggests problems with both over-reporting and under-reporting methylation sites. However, isotope labeling can be used effectively to address the issue of false-positives, and fractionation of proteins can increase the probability of identifying methylation sites in lower abundance. Here we have adapted heavy methyl SILAC to analyze fractions of the budding yeast Saccharomyces cerevisiae under respiratory conditions to allow for the production of mitochondria, an organelle whose proteins are often overlooked in larger methyl proteome studies. We have found 12 methylation sites on 11 mitochondrial proteins as well as an additional 14 methylation sites on 9 proteins that are nonmitochondrial. Of these methylation sites, 20 sites have not been previously reported. This study represents the first characterization of the yeast mitochondrial methyl proteome and the second proteomic investigation of global mitochondrial methylation to date in any organism.
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Affiliation(s)
- Katelyn E Caslavka Zempel
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - Ajay A Vashisht
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - William D Barshop
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - James A Wohlschlegel
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
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38
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Modulation of the cytoplasmic functions of mammalian post-transcriptional regulatory proteins by methylation and acetylation: a key layer of regulation waiting to be uncovered? Biochem Soc Trans 2016; 43:1285-95. [PMID: 26614674 DOI: 10.1042/bst20150172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-transcriptional control of gene expression is critical for normal cellular function and viability and many of the proteins that mediate post-transcriptional control are themselves subject to regulation by post-translational modification (PTM), e.g. phosphorylation. However, proteome-wide studies are revealing new complexities in the PTM status of mammalian proteins, in particular large numbers of novel methylated and acetylated residues are being identified. Here we review studied examples of methylation/acetylation-dependent regulation of post-transcriptional regulatory protein (PTRP) function and present collated PTM data that points to the huge potential for regulation of mRNA fate by these PTMs.
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39
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Abeykoon AH, Noinaj N, Choi BE, Wise L, He Y, Chao CC, Wang G, Gucek M, Ching WM, Chock PB, Buchanan SK, Yang DCH. Structural Insights into Substrate Recognition and Catalysis in Outer Membrane Protein B (OmpB) by Protein-lysine Methyltransferases from Rickettsia. J Biol Chem 2016; 291:19962-74. [PMID: 27474738 DOI: 10.1074/jbc.m116.723460] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/06/2022] Open
Abstract
Rickettsia belong to a family of Gram-negative obligate intracellular infectious bacteria that are the causative agents of typhus and spotted fever. Outer membrane protein B (OmpB) occurs in all rickettsial species, serves as a protective envelope, mediates host cell adhesion and invasion, and is a major immunodominant antigen. OmpBs from virulent strains contain multiple trimethylated lysine residues, whereas the avirulent strain contains mainly monomethyllysine. Two protein-lysine methyltransferases (PKMTs) that catalyze methylation of recombinant OmpB at multiple sites with varying sequences have been identified and overexpressed. PKMT1 catalyzes predominantly monomethylation, whereas PKMT2 catalyzes mainly trimethylation. Rickettsial PKMT1 and PKMT2 are unusual in that their primary substrate appears to be limited to OmpB, and both are capable of methylating multiple lysyl residues with broad sequence specificity. Here we report the crystal structures of PKMT1 from Rickettsia prowazekii and PKMT2 from Rickettsia typhi, both the apo form and in complex with its cofactor S-adenosylmethionine or S-adenosylhomocysteine. The structure of PKMT1 in complex with S-adenosylhomocysteine is solved to a resolution of 1.9 Å. Both enzymes are dimeric with each monomer containing an S-adenosylmethionine binding domain with a core Rossmann fold, a dimerization domain, a middle domain, a C-terminal domain, and a centrally located open cavity. Based on the crystal structures, residues involved in catalysis, cofactor binding, and substrate interactions were examined using site-directed mutagenesis followed by steady state kinetic analysis to ascertain their catalytic functions in solution. Together, our data reveal new structural and mechanistic insights into how rickettsial methyltransferases catalyze OmpB methylation.
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Affiliation(s)
- Amila H Abeykoon
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907,
| | - Bok-Eum Choi
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Lindsay Wise
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Yi He
- Laboratory of Biochemistry and
| | - Chien-Chung Chao
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland 20910
| | | | | | - Wei-Mei Ching
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland 20910
| | | | - Susan K Buchanan
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - David C H Yang
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057,
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40
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Al-Hadid Q, Roy K, Chanfreau G, Clarke SG. Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity. RNA (NEW YORK, N.Y.) 2016; 22:489-98. [PMID: 26826131 PMCID: PMC4793205 DOI: 10.1261/rna.054569.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/14/2015] [Indexed: 05/05/2023]
Abstract
Rpl3, a highly conserved ribosomal protein, is methylated at histidine 243 by the Hpm1 methyltransferase in Saccharomyces cerevisiae. Histidine 243 lies close to the peptidyl transferase center in a functionally important region of Rpl3 designated as the basic thumb that coordinates the decoding, peptidyl transfer, and translocation steps of translation elongation. Hpm1 was recently implicated in ribosome biogenesis and translation. However, the biological role of methylation of its Rpl3 substrate has not been identified. Here we interrogate the role of Rpl3 methylation at H243 by investigating the functional impact of mutating this histidine residue to alanine (rpl3-H243A). Akin to Hpm1-deficient cells, rpl3-H243A cells accumulate 35S and 23S pre-rRNA precursors to a similar extent, confirming an important role for histidine methylation in pre-rRNA processing. In contrast, Hpm1-deficient cells but not rpl3-H243A mutants show perturbed levels of ribosomal subunits. We show that Hpm1 has multiple substrates in different subcellular fractions, suggesting that methylation of proteins other than Rpl3 may be important for controlling ribosomal subunit levels. Finally, translational fidelity assays demonstrate that like Hpm1-deficient cells, rpl3-H243A mutants have defects in translation elongation resulting in decreased translational accuracy. These data suggest that Rpl3 methylation at H243 is playing a significant role in translation elongation, likely via the basic thumb, but has little impact on ribosomal subunit levels. Hpm1 is therefore a multifunctional methyltransferase with independent roles in ribosome biogenesis and translation.
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Affiliation(s)
- Qais Al-Hadid
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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Małecki J, Dahl HA, Moen A, Davydova E, Falnes PØ. The METTL20 Homologue from Agrobacterium tumefaciens Is a Dual Specificity Protein-lysine Methyltransferase That Targets Ribosomal Protein L7/L12 and the β Subunit of Electron Transfer Flavoprotein (ETFβ). J Biol Chem 2016; 291:9581-95. [PMID: 26929405 DOI: 10.1074/jbc.m115.709261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 12/31/2022] Open
Abstract
Human METTL20 is a mitochondrial, lysine-specific methyltransferase that methylates the β-subunit of electron transfer flavoprotein (ETFβ). Interestingly, putative METTL20 orthologues are found in a subset of α-proteobacteria, including Agrobacterium tumefaciens Using an activity-based approach, we identified in bacterial extracts two substrates of recombinant METTL20 from A. tumefaciens (AtMETTL20), namely ETFβ and the ribosomal protein RpL7/L12. We show that AtMETTL20, analogous to the human enzyme, methylates ETFβ on Lys-193 and Lys-196 both in vitro and in vivo ETF plays a key role in mediating electron transfer from various dehydrogenases, and we found that its electron transferring ability was diminished by AtMETTL20-mediated methylation of ETFβ. Somewhat surprisingly, AtMETTL20 also catalyzed monomethylation of RpL7/L12 on Lys-86, a common modification also found in many bacteria that lack METTL20. Thus, we here identify AtMETTL20 as the first enzyme catalyzing RpL7/L12 methylation. In summary, here we have identified and characterized a novel bacterial lysine-specific methyltransferase with unprecedented dual substrate specificity within the seven β-strand class of lysine-specific methyltransferases, as it targets two apparently unrelated substrates, ETFβ and RpL7/L12. Moreover, the present work establishes METTL20-mediated methylation of ETFβ as the first lysine methylation event occurring in both bacteria and humans.
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Affiliation(s)
- Jędrzej Małecki
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Helge-André Dahl
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Anders Moen
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Erna Davydova
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Pål Ø Falnes
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
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42
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Al-Hadid Q, White J, Clarke S. Ribosomal protein methyltransferases in the yeast Saccharomyces cerevisiae: Roles in ribosome biogenesis and translation. Biochem Biophys Res Commun 2016; 470:552-557. [PMID: 26801560 DOI: 10.1016/j.bbrc.2016.01.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/17/2016] [Indexed: 11/24/2022]
Abstract
A significant percentage of the methyltransferasome in Saccharomyces cerevisiae and higher eukaryotes is devoted to methylation of the translational machinery. Methylation of the RNA components of the translational machinery has been studied extensively and is important for structure stability, ribosome biogenesis, and translational fidelity. However, the functional effects of ribosomal protein methylation by their cognate methyltransferases are still largely unknown. Previous work has shown that the ribosomal protein Rpl3 methyltransferase, histidine protein methyltransferase 1 (Hpm1), is important for ribosome biogenesis and translation elongation fidelity. In this study, yeast strains deficient in each of the ten ribosomal protein methyltransferases in S. cerevisiae were examined for potential defects in ribosome biogenesis and translation. Like Hpm1-deficient cells, loss of four of the nine other ribosomal protein methyltransferases resulted in defects in ribosomal subunit synthesis. All of the mutant strains exhibited resistance to the ribosome inhibitors anisomycin and/or cycloheximide in plate assays, but not in liquid culture. Translational fidelity assays measuring stop codon readthrough, amino acid misincorporation, and programmed -1 ribosomal frameshifting, revealed that eight of the ten enzymes are important for translation elongation fidelity and the remaining two are necessary for translation termination efficiency. Altogether, these results demonstrate that ribosomal protein methyltransferases in S. cerevisiae play important roles in ribosome biogenesis and translation.
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Affiliation(s)
- Qais Al-Hadid
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Jonelle White
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Steven Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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Xia Y, Niu Y, Cui J, Fu Y, Chen XS, Lou H, Cao Q. The Helicase Activity of Hyperthermophilic Archaeal MCM is Enhanced at High Temperatures by Lysine Methylation. Front Microbiol 2015; 6:1247. [PMID: 26617586 PMCID: PMC4639711 DOI: 10.3389/fmicb.2015.01247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022] Open
Abstract
Lysine methylation and methyltransferases are widespread in the third domain of life, archaea. Nevertheless, the effects of methylation on archaeal proteins wait to be defined. Here, we report that recombinant sisMCM, an archaeal homolog of Mcm2-7 eukaryotic replicative helicase, is methylated by aKMT4 in vitro. Mono-methylation of these lysine residues occurs coincidently in the endogenous sisMCM protein purified from the hyperthermophilic Sulfolobus islandicus cells as indicated by mass spectra. The helicase activity of mini-chromosome maintenance (MCM) is stimulated by methylation, particularly at temperatures over 70°C. The methylated MCM shows optimal DNA unwinding activity after heat-treatment between 76 and 82°C, which correlates well with the typical growth temperatures of hyperthermophilic Sulfolobus. After methylation, the half life of MCM helicase is dramatically extended at 80°C. The methylated sites are located on the accessible protein surface, which might modulate the intra- and inter- molecular interactions through changing the hydrophobicity and surface charge. Furthermore, the methylation-mimic mutants of MCM show heat resistance helicase activity comparable to the methylated MCM. These data provide the biochemical evidence that posttranslational modifications such as methylation may enhance kinetic stability of proteins under the elevated growth temperatures of hyperthermophilic archaea.
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Affiliation(s)
- Yisui Xia
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Yanling Niu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Jiamin Cui
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Yang Fu
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles CA, USA ; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles CA, USA ; Department of Chemistry, University of Southern California, Los Angeles CA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles CA, USA ; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles CA, USA ; Department of Chemistry, University of Southern California, Los Angeles CA, USA
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
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Mazzoleni M, Figuet S, Martin-Laffon J, Mininno M, Gilgen A, Leroux M, Brugière S, Tardif M, Alban C, Ravanel S. Dual Targeting of the Protein Methyltransferase PrmA Contributes to Both Chloroplastic and Mitochondrial Ribosomal Protein L11 Methylation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:1697-710. [PMID: 26116422 DOI: 10.1093/pcp/pcv098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 05/09/2023]
Abstract
Methylation of ribosomal proteins has long been described in prokaryotes and eukaryotes, but our knowledge about the enzymes responsible for these modifications in plants is scarce. The bacterial protein methyltransferase PrmA catalyzes the trimethylation of ribosomal protein L11 (RPL11) at three distinct sites. The role of these modifications is still unknown. Here, we show that PrmA from Arabidopsis thaliana (AtPrmA) is dually targeted to chloroplasts and mitochondria. Mass spectrometry and enzymatic assays indicated that the enzyme methylates RPL11 in plasto- and mitoribosomes in vivo. We determined that the Arabidopsis and Escherichia coli PrmA enzymes share similar product specificity, making trimethylated residues, but, despite an evolutionary relationship, display a difference in substrate site specificity. In contrast to the bacterial enzyme that trimethylates the ε-amino group of two lysine residues and the N-terminal α-amino group, AtPrmA methylates only one lysine in the MAFCK(D/E)(F/Y)NA motif of plastidial and mitochondrial RPL11. The plant enzyme possibly methylates the N-terminus of plastidial RPL11, whereas mitochondrial RPL11 is N-α-acetylated by an unknown acetyltransferase. Lastly, we found that an Arabidopsis prma-null mutant is viable in standard environmental conditions and no molecular defect could be associated with a lack of RPL11 methylation in leaf chloroplasts or mitochondria. However, the conservation of PrmA during the evolution of photosynthetic eukaryotes together with the location of methylated residues at the binding site of translation factors to ribosomes suggests that RPL11 methylation in plant organelles could be involved, in combination with other post-translational modifications, in optimizing ribosome function.
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Affiliation(s)
- Meryl Mazzoleni
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sylvie Figuet
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Jacqueline Martin-Laffon
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Morgane Mininno
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Annabelle Gilgen
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Mélanie Leroux
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sabine Brugière
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Marianne Tardif
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Claude Alban
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Stéphane Ravanel
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
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Jakobsson ME, Davydova E, Małecki J, Moen A, Falnes PØ. Saccharomyces cerevisiae Eukaryotic Elongation Factor 1A (eEF1A) Is Methylated at Lys-390 by a METTL21-Like Methyltransferase. PLoS One 2015; 10:e0131426. [PMID: 26115316 PMCID: PMC4482628 DOI: 10.1371/journal.pone.0131426] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/01/2015] [Indexed: 01/08/2023] Open
Abstract
The human methyltransferases (MTases) METTL21A and VCP-KMT (METTL21D) were recently shown to methylate single lysine residues in Hsp70 proteins and in VCP, respectively. The yet uncharacterized MTase encoded by the YNL024C gene in Saccharomyces cerevisiae shows high sequence similarity to METTL21A and VCP-KMT, as well as to their uncharacterized paralogues METTL21B and METTL21C. Despite being most similar to METTL21A, the Ynl024c protein does not methylate yeast Hsp70 proteins, which were found to be unmethylated on the relevant lysine residue. Eukaryotic translation elongation factor eEF1A in yeast has been reported to contain four methylated lysine residues (Lys30, Lys79, Lys318 and Lys390), and we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified. Lys390 was found in a partially monomethylated state in wild-type yeast cells but was exclusively unmethylated in a ynl024cΔ strain, and over-expression of Ynl024c caused a dramatic increase in Lys390 methylation, with trimethylation becoming the predominant state. Our results demonstrate that Ynl024c is the enzyme responsible for methylation of eEF1A at Lys390, and in accordance with prior naming of similar enzymes, we suggest that Ynl024c is renamed to Efm6 (Elongation factor MTase 6).
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Affiliation(s)
- Magnus E. Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
- * E-mail: (MEJ); (PØF)
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Jędrzej Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
| | - Pål Ø. Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway
- * E-mail: (MEJ); (PØF)
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Wicker-Planquart C, Jault JM. Interaction between Bacillus subtilis YsxC and ribosomes (or rRNAs). FEBS Lett 2015; 589:1026-32. [PMID: 25771857 DOI: 10.1016/j.febslet.2015.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/04/2015] [Indexed: 11/28/2022]
Abstract
YsxC is an essential P-loop GTPase, that binds to the 50S ribosomal subunit, and is required for the proper assembly of the ribosome. The aim of this study was to characterize YsxC ribosome interactions. The stoichiometry of YsxC ribosome subunit complex was evaluated. We showed that YsxC binding to the 50S ribosomal subunit is not affected by GTP, but in the presence of GDP the stoichiometry of YsxC-ribosome is decreased. YsxC GTPase activity was stimulated upon 50S ribosomal subunit binding. In addition, it is shown for the first time that YsxC binds both 16S and 23S ribosomal RNAs.
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Affiliation(s)
- Catherine Wicker-Planquart
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France; CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France.
| | - Jean-Michel Jault
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France; CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France.
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47
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Gunawan M, Venkatesan N, Loh JT, Wong JF, Berger H, Neo WH, Li LYJ, La Win MK, Yau YH, Guo T, See PCE, Yamazaki S, Chin KC, Gingras AR, Shochat SG, Ng LG, Sze SK, Ginhoux F, Su IH. The methyltransferase Ezh2 controls cell adhesion and migration through direct methylation of the extranuclear regulatory protein talin. Nat Immunol 2015; 16:505-16. [DOI: 10.1038/ni.3125] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/12/2015] [Indexed: 12/11/2022]
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48
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Proteomic analysis of protein methylation in the yeast Saccharomyces cerevisiae. J Proteomics 2015; 114:226-33. [DOI: 10.1016/j.jprot.2014.07.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 07/09/2014] [Accepted: 07/20/2014] [Indexed: 11/23/2022]
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49
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Dzialo MC, Travaglini KJ, Shen S, Loo JA, Clarke SG. A new type of protein lysine methyltransferase trimethylates Lys-79 of elongation factor 1A. Biochem Biophys Res Commun 2014; 455:382-9. [PMID: 25446118 DOI: 10.1016/j.bbrc.2014.11.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022]
Abstract
The elongation factors of Saccharomyces cerevisiae are extensively methylated, containing a total of ten methyllysine residues. Elongation factor methyltransferases (Efm1, Efm2, Efm3, and Efm4) catalyze at least four of these modifications. Here we report the identification of a new type of protein lysine methyltransferase, Efm5 (Ygr001c), which was initially classified as N6-adenine DNA methyltransferase-like. Efm5 is required for trimethylation of Lys-79 on EF1A. We directly show the loss of this modification in efm5Δ strains by both mass spectrometry and amino acid analysis. Close homologs of Efm5 are found in vertebrates, invertebrates, and plants, although some fungal species apparently lack this enzyme. This suggests possible unique functions of this modification in S. cerevisiae and higher eukaryotes. The misannotation of Efm5 was due to the presence of a DPPF sequence in post-Motif II, typically associated with DNA methylation. Further analysis of this motif and others like it demonstrates a potential consensus sequence for N-methyltransferases.
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Affiliation(s)
- Maria C Dzialo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Kyle J Travaglini
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Sean Shen
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; Department of Biological Chemistry and UCLA/DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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50
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Kebede AF, Schneider R, Daujat S. Novel types and sites of histone modifications emerge as players in the transcriptional regulation contest. FEBS J 2014; 282:1658-74. [DOI: 10.1111/febs.13047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Adam F. Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
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