1
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Naga R, Poddar S, Bhattacharjee A, Kar P, Bose A, Mattaparthi VSK, Mukherjee O, Saha S. Structural analysis of human ATE1 isoforms and their interactions with Arg-tRNA Arg. J Biomol Struct Dyn 2024; 42:7554-7573. [PMID: 37505085 DOI: 10.1080/07391102.2023.2240449] [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: 10/10/2022] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
Posttranslational protein arginylation has been shown as a key regulator of cellular processes in eukaryotes by affecting protein stability, function, and interaction with macromolecules. Thus, the enzyme Arginyltransferase and its targets, are of immense interest to modulate cellular processes in the normal and diseased state. While the study on the effect of this posttranslational modification in mammalian systems gained momentum in the recent times, the detail structures of human ATE1 (hATE1) enzymes has not been investigated so far. Thus, the purpose of this study was to predict the overall structure and the structure function relationship of hATE1 enzyme and its four isoforms. The structure of four ATE1 isoforms were modelled and were docked with 3'end of the Arg-tRNAArg which acts as arginine donor in the arginylation reaction, followed by MD simulation. All the isoforms showed two distinct domains. A compact domain and a somewhat flexible domain as observed in the RMSF plot. A distinct similarity in the overall structure and interacting residues were observed between hATE1-1 and X4 compared to hATE1-2 and 5. While the putative active sites of all the hATE1 isoforms were located at the same pocket, differences were observed in the active site residues across hATE1 isoforms suggesting different substrate specificity. Mining of nsSNPs showed several nsSNPs including cancer associated SNPs with deleterious consequences on hATE1 structure and function. Thus, the current study for the first time shows the structural differences in the mammalian ATE1 isoforms and their possible implications in the function of these proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahul Naga
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, India
| | - Sayan Poddar
- Department of Bioscience and Biomedical Engineering, IIT Indore, Indore, India
| | - Arghyadeep Bhattacharjee
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, India
- Department of Microbiology, Kingston College of Science, Barasat, Kolkata, West Bengal, India
| | - Parimal Kar
- Department of Bioscience and Biomedical Engineering, IIT Indore, Indore, India
| | - Avishek Bose
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, India
| | | | - Oindrilla Mukherjee
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, India
| | - Sougata Saha
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, India
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2
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Lin Z, Xie Y, Gongora J, Liu X, Zahn E, Palai BB, Ramirez D, Searfoss RM, Vitorino FN, Dann GP, Zhao C, Han X, MacTaggart B, Lan X, Fu D, Greenberg L, Zhang Y, Lavine KJ, Greenberg MJ, Lv D, Kashina A, Garcia BA. An Unbiased Proteomic Platform for Activity-based Arginylation Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596974. [PMID: 38854050 PMCID: PMC11160793 DOI: 10.1101/2024.06.01.596974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Protein arginylation is an essential posttranslational modification (PTM) catalyzed by arginyl-tRNA-protein transferase 1 (ATE1) in mammalian systems. Arginylation features a post-translational conjugation of an arginyl to a protein, making it extremely challenging to differentiate from translational arginine residues with the same mass in a protein sequence. Here we present a general activity-based arginylation profiling (ABAP) platform for the unbiased discovery of arginylation substrates and their precise modification sites. This method integrates isotopic arginine labeling into an ATE1 assay utilizing biological lysates (ex vivo) rather than live cells, thus eliminating translational bias derived from the ribosomal activity and enabling bona fide arginylation identification using isotopic features. ABAP has been successfully applied to an array of peptide, protein, cell, patient, and animal tissue samples using 20 μg sample input, with 229 unique arginylation sites revealed from human proteomes. Representative sites were validated and followed up for their biological functions. The developed platform is globally applicable to the aforementioned sample types and therefore paves the way for functional studies of this difficult-to-characterize protein modification.
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Affiliation(s)
- Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Joanna Gongora
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Emily Zahn
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Bibhuti Bhusana Palai
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Daniel Ramirez
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Rick M. Searfoss
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Francisca N. Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Geoffrey P. Dann
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104
| | - Chenfeng Zhao
- McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63110
| | - Xian Han
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Brittany MacTaggart
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Xin Lan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Dechen Fu
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Lina Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Yi Zhang
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Kory J. Lavine
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael J. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Anna Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
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3
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Kashina AS, Yates Iii JR. Identification of Arginylated Proteins by Mass Spectrometry. Methods Mol Biol 2023; 2620:139-152. [PMID: 37010760 DOI: 10.1007/978-1-0716-2942-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Here, we describe the method for the identification of arginylated proteins by mass spectrometry. This method has been originally applied to the identification of N-terminally added Arg on proteins and peptides and then expanded to the side chain modification which has been recently described by our groups. The key steps in this method include the use of the mass spectrometry instruments that can identify peptides with very high pass accuracy (Orbitrap) and apply stringent mass cutoffs during automated data analysis, followed by manual validation of the identified spectra. These methods can be used with both complex and purified protein samples and, to date, constitute the only reliable way to confirm arginylation at a particular site on a protein or peptide.
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Affiliation(s)
- Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - John R Yates Iii
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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4
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Kashina AS. Protein Arginylation: Milestones of Discovery. Methods Mol Biol 2023; 2620:1-13. [PMID: 37010742 DOI: 10.1007/978-1-0716-2942-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Posttranslational modifications have emerged in recent years as the major biological regulators responsible for the orders of magnitude increase in complexity during gene expression and regulation. These "molecular switches" affect nearly every protein in vivo by modulating their structure, activity, molecular interactions, and homeostasis ultimately regulating their functions. While over 350 posttranslational modifications have been described, only a handful of them have been characterized. Until recently, protein arginylation has belonged to the list of obscure, poorly understood posttranslational modifications, before the recent explosion of studies has put arginylation on the map of intracellular metabolic pathways and biological functions. This chapter contains an overview of all the major milestones in the protein arginylation field, from its original discovery in 1963 to this day.
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Affiliation(s)
- Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Arginylation Regulates Cytoskeleton Organization and Cell Division and Affects Mitochondria in Fission Yeast. Mol Cell Biol 2022; 42:e0026122. [PMID: 36226970 PMCID: PMC9670973 DOI: 10.1128/mcb.00261-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein arginylation mediated by arginyltransferase Ate1 is a posttranslational modification of emerging importance implicated in the regulation of mammalian embryogenesis, the cardiovascular system, tissue morphogenesis, cell migration, neurodegeneration, cancer, and aging. Ate1 deletion results in embryonic lethality in mice but does not affect yeast viability, making yeast an ideal system to study the molecular pathways regulated by arginylation. Here, we conducted a global analysis of cytoskeleton-related arginylation-dependent phenotypes in Schizosaccharomyces pombe, a fission yeast species that shares many fundamental features of higher eukaryotic cells. Our studies revealed roles of Ate1 in cell division, cell polarization, organelle transport, and interphase cytoskeleton organization and dynamics. We also found a role of Ate1 in mitochondria morphology and maintenance. Furthermore, targeted mass spectrometry analysis of the total Sc. pombe arginylome identified a number of arginylated proteins, including those that play direct roles in these processes; lack of their arginylation may be responsible for ate1-knockout phenotypes. Our work outlines global biological processes potentially regulated by arginylation and paves the way to unraveling the functions of protein arginylation that are conserved at multiple levels of evolution and potentially constitute the primary role of this modification in vivo.
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6
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Functional Interplay between Arginyl-tRNA Synthetases and Arginyltransferase. Int J Mol Sci 2022; 23:ijms231710160. [PMID: 36077558 PMCID: PMC9456563 DOI: 10.3390/ijms231710160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Protein arginylation, mediated by arginyltransferase ATE1, is a post-translational modification of emerging biological importance that consists of transfer of the amino acid Arg to protein and peptide substrates. ATE1 utilizes charged tRNAArg as the donor of the arginyl group, which depends on the activity of Arg-tRNA synthetases (RARS) and is also utilized in translation. The mechanisms that regulate the functional balance among ATE1, RARS and translation are unknown. Here, we addressed the question of how these two enzymes can partition Arg-tRNAArg to functionally distinct pathways using an intracellular arginylation sensor in cell lines with overexpression or deletion of ATE1 and RARS isoforms. We found that arginylation levels depend on the physiological state of the cells but are not directly affected by translation activity or the availability of RARS isoforms. However, displacement of RARS from the multi-synthetase complex leads to an increase in intracellular arginylation independently of RARS enzymatic activity. This effect is accompanied by ATE1′s redistribution into the cytosol. Our results provide the first comprehensive analysis of the interdependence among translation, arginyl-tRNA synthesis and arginylation.
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7
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Vedula P, Tang HY, Speicher DW, Kashina A. Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma. Front Cell Dev Biol 2022; 10:807149. [PMID: 35223838 PMCID: PMC8873527 DOI: 10.3389/fcell.2022.807149] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in the past 2 years, causing a global pandemic. Here, we performed proteomic analysis of plasma samples from COVID-19 patients compared to healthy control donors in an exploratory study to gain insights into protein-level changes in the patients caused by SARS-CoV-2 infection and to identify potential proteomic and posttranslational signatures of this disease. Our results suggest a global change in protein processing and regulation that occurs in response to SARS-CoV-2, and the existence of a posttranslational COVID-19 signature that includes an elevation in threonine phosphorylation, a change in glycosylation, and a decrease in arginylation, an emerging posttranslational modification not previously implicated in infectious disease. This study provides a resource for COVID-19 researchers and, longer term, and will inform our understanding of this disease and its treatment.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States
| | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, PA, United States
| | | | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, United States,*Correspondence: Anna Kashina,
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8
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Avcilar-Kucukgoze I, MacTaggart B, Kashina A. Availability of Arg, but Not tRNA, Is a Rate-Limiting Factor for Intracellular Arginylation. Int J Mol Sci 2021; 23:314. [PMID: 35008737 PMCID: PMC8745564 DOI: 10.3390/ijms23010314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Protein arginylation, mediated by arginyltransferase ATE1, is a posttranslational modification of emerging biological importance that consists of transfer of the amino acid Arg from tRNA to protein and peptide targets. ATE1 can bind tRNA and exhibits specificity toward particular tRNA types, but its dependence on the availability of the major components of the arginylation reaction has never been explored. Here we investigated key intracellular factors that can potentially regulate arginylation in vivo, including several tRNA types that show strong binding to ATE1, as well as availability of free Arg, in an attempt to identify intracellular rate limiting steps for this enzyme. Our results demonstrate that, while modulation of tRNA levels in cells does not lead to any changes in intracellular arginylation efficiency, availability of free Arg is a potentially rate-limiting factor that facilitates arginylation if added to the cultured cells. Our results broadly outline global pathways that may be involved in the regulation of arginylation in vivo.
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Affiliation(s)
| | | | - Anna Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (I.A.-K.); (B.M.)
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9
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Xu C, Li YM, Sun B, Zhong FJ, Yang LY. ATE1 Inhibits Liver Cancer Progression through RGS5-Mediated Suppression of Wnt/β-Catenin Signaling. Mol Cancer Res 2021; 19:1441-1453. [PMID: 34158395 PMCID: PMC9398136 DOI: 10.1158/1541-7786.mcr-21-0027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/04/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Arginyltransferase (ATE1) plays critical roles in many biological functions including cardiovascular development, angiogenesis, adipogenesis, muscle contraction, and metastasis of cancer. However, the role of ATE1 in hepatocellular carcinoma (HCC) remains unknown. In this study, we find that ATE1 plays an essential role in growth and malignancy of liver cancer. ATE1 expression is significantly reduced in human HCC samples compared with normal liver tissue. In addition, low ATE1 expression is correlated with aggressive clinicopathologic features and is an independent poor prognostic factor for overall survival and disease-free survival of patients with HCC. Lentivirus-mediated ATE1 knockdown significantly promoted liver cancer growth, migration, and disease progression in vitro and in vivo. Opposing results were observed when ATE1 was upregulated. Mechanistically, ATE1 accelerated the degradation of β-catenin and inhibited Wnt signaling by regulating turnover of Regulator of G Protein Signaling 5 (RGS5). Loss- and gain-of-function assays confirmed that RGS5 was a key effector of ATE1-mediated regulation of Wnt signaling. Further studies indicated that RGS5 might be involved in regulating the activity of GSK3-β, a crucial component of the cytoplasmic destruction complex. Treatment with a GSK inhibitor (CHIR99021) cooperated with ablation of ATE1 or RGS5 overexpression to promote Wnt/β-catenin signaling, but overexpression of ATE1 or RGS5 knockdown did not reverse the effect of GSK inhibitor. IMPLICATIONS: ATE1 inhibits liver cancer progression by suppressing Wnt/β-catenin signaling and can serve as a potentially valuable prognostic biomarker for HCC.
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Affiliation(s)
- Cong Xu
- Liver Cancer Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi-Ming Li
- Liver Cancer Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo Sun
- Liver Cancer Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang-Jing Zhong
- Liver Cancer Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lian-Yue Yang
- Liver Cancer Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Corresponding Author: Lian-Yue Yang, Department of Surgery, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, Hunan 410008, China. Phone: 731-8432-7365; Fax: 731-8432-7618; E-mail:
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10
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Wiley DJ, D’Urso G, Zhang F. Posttranslational Arginylation Enzyme Arginyltransferase1 Shows Genetic Interactions With Specific Cellular Pathways in vivo. Front Physiol 2020; 11:427. [PMID: 32435206 PMCID: PMC7218141 DOI: 10.3389/fphys.2020.00427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/07/2020] [Indexed: 12/20/2022] Open
Abstract
Arginyltransferase1 (ATE1) is a conserved enzyme in eukaryotes mediating posttranslational arginylation, the addition of an extra arginine to an existing protein. In mammals, the dysregulations of the ATE1 gene (ate1) is shown to be involved in cardiovascular abnormalities, cancer, and aging-related diseases. Although biochemical evidence suggested that arginylation may be involved in stress response and/or protein degradation, the physiological role of ATE1 in vivo has never been systematically determined. This gap of knowledge leads to difficulties for interpreting the involvements of ATE1 in diseases pathogenesis. Since ate1 is highly conserved between human and the unicellular organism Schizosaccharomyces pombe (S. pombe), we take advantage of the gene-knockout library of S. pombe, to investigate the genetic interactions between ate1 and other genes in a systematic and unbiased manner. By this approach, we found that ate1 has a surprisingly small and focused impact size. Among the 3659 tested genes, which covers nearly 75% of the genome of S. pombe, less than 5% of them displayed significant genetic interactions with ate1. Furthermore, these ate1-interacting partners can be grouped into a few discrete clustered categories based on their functions or their physical interactions. These categories include translation/transcription regulation, biosynthesis/metabolism of biomolecules (including histidine), cell morphology and cellular dynamics, response to oxidative or metabolic stress, ribosomal structure and function, and mitochondrial function. Unexpectedly, inconsistent to popular belief, very few genes in the global ubiquitination or degradation pathways showed interactions with ate1. Our results suggested that ATE1 specifically regulates a handful of cellular processes in vivo, which will provide critical mechanistic leads for studying the involvements of ATE1 in normal physiologies as well as in diseased conditions.
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Affiliation(s)
- David J. Wiley
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
| | - Gennaro D’Urso
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
| | - Fangliang Zhang
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
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11
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Abstract
Protein arginylation-enzymatic addition of the amino acid arginine (Arg) to proteins, mediated by arginyltransferase ATE1, has been discovered in 1963, but is still relatively poorly understood. Studies of arginylation present many technical challenges, which arise from the fact that Arg is a regular amino acid that also incorporates into proteins during translation. Thus, in vitro arginylation needs to be conducted in a strictly ribosome-free system, in highly controlled conditions. Identification of arginylated proteins is currently only possible by high precision mass spectrometry, which relies on very high mass accuracy of the instruments, specific ionization patterns during mass fragmentation, as well as multiple stringent steps of automated and manual validation. Below we describe the methods of in vitro arginylation and mass spectrometry analysis of arginylated proteins, developed by our groups during the last 15 years.
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Affiliation(s)
- Junling Wang
- University of Pennsylvania, Philadelphia, PA, United States
| | - John R Yates
- The Scripps Research Institute, LaJolla, CA, United States
| | - Anna Kashina
- University of Pennsylvania, Philadelphia, PA, United States.
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12
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Rassier DE, Kashina A. Protein arginylation of cytoskeletal proteins in the muscle: modifications modifying function. Am J Physiol Cell Physiol 2019; 316:C668-C677. [PMID: 30789755 PMCID: PMC6580163 DOI: 10.1152/ajpcell.00500.2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/30/2022]
Abstract
The cytoskeleton drives many essential processes in normal physiology, and its impairments underlie many diseases, including skeletal myopathies, cancer, and heart failure, that broadly affect developed countries worldwide. Cytoskeleton regulation is a field of investigation of rapidly emerging global importance and a new venue for the development of potential therapies. This review overviews our present understanding of the posttranslational regulation of the muscle cytoskeleton through arginylation, a tRNA-dependent addition of arginine to proteins mediated by arginyltransferase 1. We focus largely on arginylation-dependent regulation of striated muscles, shown to play critical roles in facilitating muscle integrity, contractility, regulation, and strength.
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Affiliation(s)
- Dilson E Rassier
- Department of Kinesiology and Physical Education, McGill University , Montreal, Quebec , Canada
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania , Philadelphia, Pennsylvania
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13
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Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A. Target site specificity and in vivo complexity of the mammalian arginylome. Sci Rep 2018; 8:16177. [PMID: 30385798 PMCID: PMC6212499 DOI: 10.1038/s41598-018-34639-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/22/2018] [Indexed: 01/16/2023] Open
Abstract
Protein arginylation mediated by arginyltransferase ATE1 is a key regulatory process essential for mammalian embryogenesis, cell migration, and protein regulation. Despite decades of studies, very little is known about the specificity of ATE1-mediated target site recognition. Here, we used in vitro assays and computational analysis to dissect target site specificity of mouse arginyltransferases and gain insights into the complexity of the mammalian arginylome. We found that the four ATE1 isoforms have different, only partially overlapping target site specificity that includes more variability in the target residues than previously believed. Based on all the available data, we generated an algorithm for identifying potential arginylation consensus motif and used this algorithm for global prediction of proteins arginylated in vivo on the N-terminal D and E. Our analysis reveals multiple proteins with potential ATE1 target sites and expand our understanding of the biological complexity of the intracellular arginylome.
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Affiliation(s)
- Junling Wang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vikas Rao Pejaver
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
- Department of Biomedical Informatics and Medical Education and the eScience Institute, University of Washington, Washington, USA
| | - Geoffrey P Dann
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Max Y Wolf
- Broad Institute of MIT and Harvard, and MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, and MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Yun Huang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA.
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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14
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Leite FDS, Kashina A, Rassier DE. Posttranslational Arginylation Regulates Striated Muscle Function. Exerc Sport Sci Rev 2018; 44:98-103. [PMID: 27111480 DOI: 10.1249/jes.0000000000000079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Felipe de Souza Leite
- 1Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, Quebec, Canada; and 2Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
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15
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Affiliation(s)
- Kamalakshi Deka
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Assam 784028, India
| | - Sougata Saha
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Assam 784028, India
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16
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Deka K, Singh A, Chakraborty S, Mukhopadhyay R, Saha S. Protein arginylation regulates cellular stress response by stabilizing HSP70 and HSP40 transcripts. Cell Death Discov 2016; 2:16074. [PMID: 27752365 PMCID: PMC5045964 DOI: 10.1038/cddiscovery.2016.74] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/23/2016] [Indexed: 01/29/2023] Open
Abstract
ATE1-mediated post-translational addition of arginine to a protein has been shown to regulate activity, interaction, and stability of the protein substrates. Arginylation has been linked to many different stress conditions, namely ER stress, cytosolic misfolded protein stress, and nitrosative stress. However, clear understanding about the effect of arginylation in cellular stress responses is yet to emerge. In this study, we investigated the role of arginylation in heat-stress response. Our findings suggest that Ate1 knock out (KO) cells are more susceptible to heat stress compared with its wild-type counterparts due to the induction of apoptosis in KO cells. Gene expression analysis of inducible heat-shock proteins (HSP70.1, HSP70.3, and HSP40) showed induction of these genes in KO cells early in the heat shock, but were drastically diminished at the later period of heat shock. Further analysis revealed that loss of ATE1 drastically reduced the stability of all three HSP mRNAs. These phenotypes were greatly restored by overexpression of Ate1 in KO cells. Our findings show that arginylation plays a protective role during heat stress by regulating HSP gene expression and mRNA stability.
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Affiliation(s)
- Kamalakshi Deka
- Department of Molecular Biology and Biotechnology, Tezpur University , Napaam, Assam, India
| | - Archana Singh
- Department of Molecular Biology and Biotechnology, Tezpur University , Napaam, Assam, India
| | - Surajit Chakraborty
- Department of Molecular Biology and Biotechnology, Tezpur University , Napaam, Assam, India
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University , Napaam, Assam, India
| | - Sougata Saha
- Department of Molecular Biology and Biotechnology, Tezpur University , Napaam, Assam, India
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17
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Wadas B, Piatkov KI, Brower CS, Varshavsky A. Analyzing N-terminal Arginylation through the Use of Peptide Arrays and Degradation Assays. J Biol Chem 2016; 291:20976-20992. [PMID: 27510035 DOI: 10.1074/jbc.m116.747956] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/29/2023] Open
Abstract
Nα-terminal arginylation (Nt-arginylation) of proteins is mediated by the Ate1 arginyltransferase (R-transferase), a component of the Arg/N-end rule pathway. This proteolytic system recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. The definitively identified ("canonical") residues that are Nt-arginylated by R-transferase are N-terminal Asp, Glu, and (oxidized) Cys. Over the last decade, several publications have suggested (i) that Ate1 can also arginylate non-canonical N-terminal residues; (ii) that Ate1 is capable of arginylating not only α-amino groups of N-terminal residues but also γ-carboxyl groups of internal (non-N-terminal) Asp and Glu; and (iii) that some isoforms of Ate1 are specific for substrates bearing N-terminal Cys residues. In the present study, we employed arrays of immobilized 11-residue peptides and pulse-chase assays to examine the substrate specificity of mouse R-transferase. We show that amino acid sequences immediately downstream of a substrate's canonical (Nt-arginylatable) N-terminal residue, particularly a residue at position 2, can affect the rate of Nt-arginylation by R-transferase and thereby the rate of degradation of a substrate protein. We also show that the four major isoforms of mouse R-transferase have similar Nt-arginylation specificities in vitro, contrary to the claim about the specificity of some Ate1 isoforms for N-terminal Cys. In addition, we found no evidence for a significant activity of the Ate1 R-transferase toward previously invoked non-canonical N-terminal or internal amino acid residues. Together, our results raise technical concerns about earlier studies that invoked non-canonical arginylation specificities of Ate1.
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Affiliation(s)
- Brandon Wadas
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Konstantin I Piatkov
- the Center for Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow 143026, Russia, and
| | | | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
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18
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Galiano MR, Goitea VE, Hallak ME. Post-translational protein arginylation in the normal nervous system and in neurodegeneration. J Neurochem 2016; 138:506-17. [PMID: 27318192 DOI: 10.1111/jnc.13708] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/24/2016] [Accepted: 06/13/2016] [Indexed: 02/07/2023]
Abstract
Post-translational arginylation of proteins is an important regulator of many physiological pathways in cells. This modification was originally noted in protein degradation during neurodegenerative processes, with an apparently different physiological relevance between central and peripheral nervous system. Subsequent studies have identified a steadily increasing number of proteins and proteolysis-derived polypeptides as arginyltransferase (ATE1) substrates, including β-amyloid, α-synuclein, and TDP43 proteolytic fragments. Arginylation is involved in signaling processes of proteins and polypeptides that are further ubiquitinated and degraded by the proteasome. In addition, it is also implicated in autophagy/lysosomal degradation pathway. Recent studies using mutant mouse strains deficient in ATE1 indicate additional roles of this modification in neuronal physiology. As ATE1 is capable of modifying proteins either at the N-terminus or middle-chain acidic residues, determining which proteins function are modulated by arginylation represents a big challenge. Here, we review studies addressing various roles of ATE1 activity in nervous system function, and suggest future research directions that will clarify the role of post-translational protein arginylation in brain development and various neurological disorders. Arginyltransferase (ATE1), the enzyme responsible for post-translational arginylation, modulates the functions of a wide variety of proteins and polypeptides, and is also involved in the main degradation pathways of intracellular proteins. Regulatory roles of ATE1 have been well defined for certain organs. However, its roles in nervous system development and neurodegenerative processes remain largely unknown, and present exciting opportunities for future research, as discussed in this review.
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Affiliation(s)
- Mauricio R Galiano
- Centro de Investigaciones de Química Biológica de Córdoba, CIQUIBIC, Departamento de Química Biológica, Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Victor E Goitea
- Centro de Investigaciones de Química Biológica de Córdoba, CIQUIBIC, Departamento de Química Biológica, Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Marta E Hallak
- Centro de Investigaciones de Química Biológica de Córdoba, CIQUIBIC, Departamento de Química Biológica, Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
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19
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Galiano MR, Hallak ME. Assaying the Posttranslational Arginylation of Proteins in Cultured Cells. Methods Mol Biol 2016; 1337:49-58. [PMID: 26285880 DOI: 10.1007/978-1-4939-2935-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To evaluate the posttranslational arginylation of proteins in vivo, we describe a protocol for studying the (14)C-Arg incorporation into proteins of cells in culture. The conditions determined for this particular modification contemplate both the biochemical requirements of the enzyme ATE1 and the adjustments that allowed the discrimination between posttranslational arginylation of proteins and de novo synthesis. These conditions are applicable for different cell lines or primary cultures, representing an optimal procedure for the identification and the validation of putative ATE1 substrates.
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Affiliation(s)
- Mauricio R Galiano
- Departamento de Química Biológica, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, (UNC-CONICET), Universidad Nacional de Córdoba (X5000HUA), Córdoba, Argentina
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20
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Abstract
Here we describe the method for identification of arginylated proteins by mass spectrometry. This method has been originally applied to the identification of N-terminally added Arg on proteins and peptides, and then expanded to identification of side chain arginylation which has been recently described by our groups. The key steps in this method include the use of the mass spectrometry instruments that can identify peptides with very high pass accuracy (Orbitrap) and apply stringent mass cutoffs during automated data analysis, followed by manual validation of the identified spectra. These methods can be used with both complex and purified protein samples and, to date, constitute the only reliable way to confirm arginylation at a particular site on a protein or peptide.
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Affiliation(s)
- Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA, 19104, USA
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21
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Hoernstein SNW, Mueller SJ, Fiedler K, Schuelke M, Vanselow JT, Schuessele C, Lang D, Nitschke R, Igloi GL, Schlosser A, Reski R. Identification of Targets and Interaction Partners of Arginyl-tRNA Protein Transferase in the Moss Physcomitrella patens. Mol Cell Proteomics 2016; 15:1808-22. [PMID: 27067052 DOI: 10.1074/mcp.m115.057190] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 12/15/2022] Open
Abstract
Protein arginylation is a posttranslational modification of both N-terminal amino acids of proteins and sidechain carboxylates and can be crucial for viability and physiology in higher eukaryotes. The lack of arginylation causes severe developmental defects in moss, affects the low oxygen response in Arabidopsis thaliana and is embryo lethal in Drosophila and in mice. Although several studies investigated impact and function of the responsible enzyme, the arginyl-tRNA protein transferase (ATE) in plants, identification of arginylated proteins by mass spectrometry was not hitherto achieved. In the present study, we report the identification of targets and interaction partners of ATE in the model plant Physcomitrella patens by mass spectrometry, employing two different immuno-affinity strategies and a recently established transgenic ATE:GUS reporter line (Schuessele et al., 2016 New Phytol. , DOI: 10.1111/nph.13656). Here we use a commercially available antibody against the fused reporter protein (β-glucuronidase) to pull down ATE and its interacting proteins and validate its in vivo interaction with a class I small heatshock protein via Förster resonance energy transfer (FRET). Additionally, we apply and modify a method that already successfully identified arginylated proteins from mouse proteomes by using custom-made antibodies specific for N-terminal arginine. As a result, we identify four arginylated proteins from Physcomitrella patens with high confidence.Data are available via ProteomeXchange with identifier PXD003228 and PXD003232.
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Affiliation(s)
- Sebastian N W Hoernstein
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Stefanie J Mueller
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Kathrin Fiedler
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Marc Schuelke
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Jens T Vanselow
- §Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Christian Schuessele
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Daniel Lang
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Roland Nitschke
- ¶ZBSA - Centre for Biological Systems Analysis, Life Imaging Center, University Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany; ‡‡BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Gabor L Igloi
- ‖Institute of Biology 3, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Andreas Schlosser
- §Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Ralf Reski
- From the ‡Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; ¶ZBSA - Centre for Biological Systems Analysis, Life Imaging Center, University Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany; **FRIAS - Freiburg Institute for Advanced Studies, 79104 Freiburg, Germany; ‡‡BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
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22
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Rai R, Zhang F, Colavita K, Leu NA, Kurosaka S, Kumar A, Birnbaum MD, Győrffy B, Dong DW, Shtutman M, Kashina A. Arginyltransferase suppresses cell tumorigenic potential and inversely correlates with metastases in human cancers. Oncogene 2015; 35:4058-68. [PMID: 26686093 PMCID: PMC4916053 DOI: 10.1038/onc.2015.473] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 11/09/2015] [Accepted: 11/14/2015] [Indexed: 02/07/2023]
Abstract
Arginylation is an emerging post-translational modification mediated by arginyltransferase (ATE1) that is essential for mammalian embryogenesis and regulation of the cytoskeleton. Here, we discovered that Ate1-knockout (KO) embryonic fibroblasts exhibit tumorigenic properties, including abnormally rapid contact-independent growth, reduced ability to form cell-cell contacts and chromosomal aberrations. Ate1-KO fibroblasts can form large colonies in Matrigel and exhibit invasive behavior, unlike wild-type fibroblasts. Furthermore, Ate1-KO cells form tumors in subcutaneous xenograft assays in immunocompromised mice. Abnormal growth in these cells can be partially rescued by reintroduction of stably expressed specific Ate1 isoforms, which also reduce the ability of these cells to form tumors. Tumor array studies and bioinformatics analysis show that Ate1 is downregulated in several types of human cancer samples at the protein level, and that its transcription level inversely correlates with metastatic progression and patient survival. We conclude that Ate1-KO results in carcinogenic transformation of cultured fibroblasts, suggesting that in addition to its previously known activities Ate1 gene is essential for tumor suppression and also likely participates in suppression of metastatic growth.
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Affiliation(s)
- R Rai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - F Zhang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K Colavita
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N A Leu
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S Kurosaka
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Kumar
- Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M D Birnbaum
- Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - B Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - D W Dong
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Shtutman
- University of South Carolina, Columbia, SC, USA
| | - A Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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23
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Leite FS, Minozzo FC, Kalganov A, Cornachione AS, Cheng YS, Leu NA, Han X, Saripalli C, Yates JR, Granzier H, Kashina AS, Rassier DE. Reduced passive force in skeletal muscles lacking protein arginylation. Am J Physiol Cell Physiol 2015; 310:C127-35. [PMID: 26511365 DOI: 10.1152/ajpcell.00269.2015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/28/2015] [Indexed: 11/22/2022]
Abstract
Arginylation is a posttranslational modification that plays a global role in mammals. Mice lacking the enzyme arginyltransferase in skeletal muscles exhibit reduced contractile forces that have been linked to a reduction in myosin cross-bridge formation. The role of arginylation in passive skeletal myofibril forces has never been investigated. In this study, we used single sarcomere and myofibril measurements and observed that lack of arginylation leads to a pronounced reduction in passive forces in skeletal muscles. Mass spectrometry indicated that skeletal muscle titin, the protein primarily linked to passive force generation, is arginylated on five sites located within the A band, an important area for protein-protein interactions. We propose a mechanism for passive force regulation by arginylation through modulation of protein-protein binding between the titin molecule and the thick filament. Key points are as follows: 1) active and passive forces were decreased in myofibrils and single sarcomeres isolated from muscles lacking arginyl-tRNA-protein transferase (ATE1). 2) Mass spectrometry revealed five sites for arginylation within titin molecules. All sites are located within the A-band portion of titin, an important region for protein-protein interactions. 3) Our data suggest that arginylation of titin is required for proper passive force development in skeletal muscles.
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Affiliation(s)
- Felipe S Leite
- Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada
| | - Fábio C Minozzo
- Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada
| | - Albert Kalganov
- Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada
| | - Anabelle S Cornachione
- Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada
| | - Yu-Shu Cheng
- Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada
| | - Nicolae A Leu
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xuemei Han
- The Scripps Research Institute, Department of Chemical Physiology, La Jolla, California
| | - Chandra Saripalli
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona; and
| | - John R Yates
- The Scripps Research Institute, Department of Chemical Physiology, La Jolla, California
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona; and
| | - Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dilson E Rassier
- Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada; Departments of Physics and Physiology, McGill University, Montreal, Quebec, Canada
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24
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Arginylation regulates purine nucleotide biosynthesis by enhancing the activity of phosphoribosyl pyrophosphate synthase. Nat Commun 2015; 6:7517. [PMID: 26175007 PMCID: PMC4503932 DOI: 10.1038/ncomms8517] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/16/2015] [Indexed: 01/31/2023] Open
Abstract
Protein arginylation is an emerging post-translational modification that targets a number of metabolic enzymes; however, the mechanisms and downstream effects of this modification are unknown. Here we show that lack of arginylation renders cells vulnerable to purine nucleotide synthesis inhibitors and affects the related glycine and serine biosynthesis pathways. We show that the purine nucleotide biosynthesis enzyme PRPS2 is selectively arginylated, unlike its close homologue PRPS1, and that arginylation of PRPS2 directly facilitates its biological activity. Moreover, selective arginylation of PRPS2 but not PRPS1 is regulated through a coding sequence-dependent mechanism that combines elements of mRNA secondary structure with lysine residues encoded near the N-terminus of PRPS1. This mechanism promotes arginylation-specific degradation of PRPS1 and selective retention of arginylated PRPS2 in vivo. We therefore demonstrate that arginylation affects both the activity and stability of a major metabolic enzyme.
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25
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Fuhrmann J, Clancy K, Thompson PR. Chemical biology of protein arginine modifications in epigenetic regulation. Chem Rev 2015; 115:5413-61. [PMID: 25970731 PMCID: PMC4463550 DOI: 10.1021/acs.chemrev.5b00003] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kathleen
W. Clancy
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
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26
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Kashina A. Protein arginylation, a global biological regulator that targets actin cytoskeleton and the muscle. Anat Rec (Hoboken) 2015; 297:1630-6. [PMID: 25125176 DOI: 10.1002/ar.22969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Posttranslational addition of Arg to proteins, mediated by arginyltransferase ATE1 has been first observed in 1963 and remained poorly understood for decades since its original discovery. Recent work demonstrated the global nature of arginylation and its essential role in multiple physiological pathways during embryogenesis and adulthood and identified over a hundred of proteins arginylated in vivo. Among these proteins, the prominent role belongs to the actin cytoskeleton and the muscle, and follow up studies strongly suggests that arginylation constitutes a novel biological regulator of contractility. This review presents an overview of the studies of protein arginylation that led to the discovery of its major role in the muscle.
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Affiliation(s)
- Anna Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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27
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Abstract
Posttranslational modifications have emerged in recent years as the major biological regulators responsible for the orders of magnitude increase in complexity of protein functions. These "molecular switches" affect nearly every protein in vivo by modulating their protein structure, activity, molecular interactions, and homeostasis. While over 350 protein modifications have been described, only a handful of them have been characterized. Until recently, protein arginylation has belonged to the list of obscure, poorly understood posttranslational modifications, before the recent explosion of studies has put arginylation on the map of intracellular metabolic pathways and biological processes. This chapter contains an overview of all the major milestones in the protein arginylation field, from its original discovery in 1963 to this day.
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28
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Cornachione AS, Leite FS, Wang J, Leu NA, Kalganov A, Volgin D, Han X, Xu T, Cheng YS, Yates JRR, Rassier DE, Kashina A. Arginylation of myosin heavy chain regulates skeletal muscle strength. Cell Rep 2014; 8:470-6. [PMID: 25017061 PMCID: PMC4126752 DOI: 10.1016/j.celrep.2014.06.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/02/2014] [Accepted: 06/13/2014] [Indexed: 11/16/2022] Open
Abstract
Protein arginylation is a posttranslational modification with an emerging global role in the regulation of actin cytoskeleton. To test the role of arginylation in the skeletal muscle, we generated a mouse model with Ate1 deletion driven by the skeletal muscle-specific creatine kinase (Ckmm) promoter. Ckmm-Ate1 mice were viable and outwardly normal; however, their skeletal muscle strength was significantly reduced in comparison to controls. Mass spectrometry of isolated skeletal myofibrils showed a limited set of proteins, including myosin heavy chain, arginylated on specific sites. Atomic force microscopy measurements of contractile strength in individual myofibrils and isolated myosin filaments from these mice showed a significant reduction of contractile forces, which, in the case of myosin filaments, could be fully rescued by rearginylation with purified Ate1. Our results demonstrate that arginylation regulates force production in muscle and exerts a direct effect on muscle strength through arginylation of myosin.
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Affiliation(s)
- Anabelle S Cornachione
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Felipe S Leite
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Junling Wang
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Nicolae A Leu
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Albert Kalganov
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Denys Volgin
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Xuemei Han
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tao Xu
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu-Shu Cheng
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | | | - Dilson E Rassier
- Department of Kinesiology and Physical Education, Physics and Physiology, McGill University, Montreal, QC H2W 1S4, Canada
| | - Anna Kashina
- Department of Animal Biology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.
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29
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Wang J, Han X, Wong CCL, Cheng H, Aslanian A, Xu T, Leavis P, Roder H, Hedstrom L, Yates JR, Kashina A. Arginyltransferase ATE1 catalyzes midchain arginylation of proteins at side chain carboxylates in vivo. ACTA ACUST UNITED AC 2014; 21:331-7. [PMID: 24529990 DOI: 10.1016/j.chembiol.2013.12.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/20/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
Abstract
Arginylation is an emerging posttranslational modification mediated by Arg-tRNA-protein-transferase (ATE1). It is believed that ATE1 links Arg solely to the N terminus of proteins, requiring prior proteolysis or action by Met-aminopeptidases to expose the arginylated site. Here, we tested the possibility of Arg linkage to midchain sites within intact protein targets and found that many proteins in vivo are modified on the side chains of Asp and Glu by unconventional chemistry that targets the carboxy rather than the amino groups at the target sites. Such arginylation appears to be functionally regulated, and it can be directly mediated by ATE1, in addition to the more conventional ATE1-mediated linkage of Arg to the N-terminal alpha amino group. This midchain arginylation implies an unconventional mechanism of ATE1 action that likely facilitates its major biological role.
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Affiliation(s)
- Junling Wang
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Xuemei Han
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Catherine C L Wong
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hong Cheng
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Aaron Aslanian
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tao Xu
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paul Leavis
- Tufts University School of Medicine, 145 Harrison Avenue, Boston, MA 02111, USA
| | - Heinrich Roder
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Lizbeth Hedstrom
- Department of Biology and Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - John R Yates
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anna Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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30
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Abstract
Many of the best-studied actin regulatory proteins use non-covalent means to modulate the properties of actin. Yet, actin is also susceptible to covalent modifications of its amino acids. Recent work is increasingly revealing that actin processing and its covalent modifications regulate important cellular events. In addition, numerous pathogens express enzymes that specifically use actin as a substrate to regulate their hosts' cells. Actin post-translational alterations have been linked to different normal and disease processes and the effects associated with metabolic and environmental stressors. Herein, we highlight specific co-translational and post-translational modifications of actin and discuss the current understanding of the role that these modifications play in regulating actin.
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Affiliation(s)
- Jonathan R Terman
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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31
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Carvalho PC, Fischer JSG, Xu T, Cociorva D, Balbuena TS, Valente RH, Perales J, Yates JR, Barbosa VC. Search engine processor: Filtering and organizing peptide spectrum matches. Proteomics 2012; 12:944-9. [PMID: 22311825 DOI: 10.1002/pmic.201100529] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The search engine processor (SEPro) is a tool for filtering, organizing, sharing, and displaying peptide spectrum matches. It employs a novel three-tier Bayesian approach that uses layers of spectrum, peptide, and protein logic to lead the data to converge to a single list of reliable protein identifications. SEPro is integrated into the PatternLab for proteomics environment, where an arsenal of tools for analyzing shotgun proteomic data is provided. By using the semi-labeled decoy approach for benchmarking, we show that SEPro significantly outperforms a commercially available competitor.
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Affiliation(s)
- Paulo C Carvalho
- Laboratory for Toxinology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
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32
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Kurosaka S, Leu NA, Pavlov I, Han X, Ribeiro PAB, Xu T, Bunte R, Saha S, Wang J, Cornachione A, Mai W, Yates JR, Rassier DE, Kashina A. Arginylation regulates myofibrils to maintain heart function and prevent dilated cardiomyopathy. J Mol Cell Cardiol 2012; 53:333-41. [PMID: 22626847 DOI: 10.1016/j.yjmcc.2012.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/25/2012] [Accepted: 05/12/2012] [Indexed: 01/25/2023]
Abstract
Protein arginylation mediated by arginyltransferase (ATE1) is essential for heart formation during embryogenesis, however its cell-autonomous role in cardiomyocytes and the differentiated heart muscle has never been investigated. To address this question, we generated cardiac muscle-specific Ate1 knockout mice, in which Ate1 deletion was driven by α-myosin heavy chain promoter (αMHC-Ate1 mouse). These mice were initially viable, but developed severe cardiac contractility defects, dilated cardiomyopathy, and thrombosis over time, resulting in high rates of lethality after 6months of age. These symptoms were accompanied by severe ultrastructural defects in cardiac myofibrils, seen in the newborns and far preceding the onset of cardiomyopathy, suggesting that these defects were primary and likely underlay the development of the future heart defects. Several major sarcomeric proteins were arginylated in vivo. Moreover, Ate1 deletion in the hearts resulted in a significant reduction of active and passive myofibril forces, suggesting that arginylation is critical for both myofibril structural integrity and contractility. Thus, arginylation is essential for maintaining the heart function by regulation of the major myofibril proteins and myofibril forces, and its absence in the heart muscle leads to progressive heart failure through cardiomyocyte-specific defects.
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Affiliation(s)
- Satoshi Kurosaka
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia 19104, USA
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