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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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Bonnet LV, Palandri A, Flores-Martin JB, Hallak ME. Arginyltransferase 1 modulates p62-driven autophagy via mTORC1/AMPk signaling. Cell Commun Signal 2024; 22:87. [PMID: 38297346 PMCID: PMC10832197 DOI: 10.1186/s12964-024-01499-9] [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: 09/21/2023] [Accepted: 01/21/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Arginyltransferase (Ate1) orchestrates posttranslational protein arginylation, a pivotal regulator of cellular proteolytic processes. In eukaryotic cells, two interconnected systems-the ubiquitin proteasome system (UPS) and macroautophagy-mediate proteolysis and cooperate to maintain quality protein control and cellular homeostasis. Previous studies have shown that N-terminal arginylation facilitates protein degradation through the UPS. Dysregulation of this machinery triggers p62-mediated autophagy to ensure proper substrate processing. Nevertheless, how Ate1 operates through this intricate mechanism remains elusive. METHODS We investigated Ate1 subcellular distribution through confocal microscopy and biochemical assays using cells transiently or stably expressing either endogenous Ate1 or a GFP-tagged Ate1 isoform transfected in CHO-K1 or MEFs, respectively. To assess Ate1 and p62-cargo clustering, we analyzed their colocalization and multimerization status by immunofluorescence and nonreducing immunoblotting, respectively. Additionally, we employed Ate1 KO cells to examine the role of Ate1 in autophagy. Ate1 KO MEFs cells stably expressing GFP-tagged Ate1-1 isoform were used as a model for phenotype rescue. Autophagy dynamics were evaluated by analyzing LC3B turnover and p62/SQSTM1 levels under both steady-state and serum-starvation conditions, through immunoblotting and immunofluorescence. We determined mTORC1/AMPk activation by assessing mTOR and AMPk phosphorylation through immunoblotting, while mTORC1 lysosomal localization was monitored by confocal microscopy. RESULTS Here, we report a multifaceted role for Ate1 in the autophagic process, wherein it clusters with p62, facilitates autophagic clearance, and modulates its signaling. Mechanistically, we found that cell-specific inactivation of Ate1 elicits overactivation of the mTORC1/AMPk signaling hub that underlies a failure in autophagic flux and subsequent substrate accumulation, which is partially rescued by ectopic expression of Ate1. Statistical significance was assessed using a two-sided unpaired t test with a significance threshold set at P<0.05. CONCLUSIONS Our findings uncover a critical housekeeping role of Ate1 in mTORC1/AMPk-regulated autophagy, as a potential therapeutic target related to this pathway, that is dysregulated in many neurodegenerative and cancer diseases.
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Affiliation(s)
- Laura V Bonnet
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina.
| | - Anabela Palandri
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
| | - Jesica B Flores-Martin
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
| | - Marta E Hallak
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina.
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3
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MacTaggart B, Shimogawa M, Lougee M, Tang HY, Petersson EJ, Kashina A. Global Analysis of Post-Translational Side-Chain Arginylation Using Pan-Arginylation Antibodies. Mol Cell Proteomics 2023; 22:100664. [PMID: 37832787 PMCID: PMC10656225 DOI: 10.1016/j.mcpro.2023.100664] [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: 03/03/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Arginylation is a post-translational modification mediated by the arginyltransferase 1 (ATE1), which transfers the amino acid arginine to a protein or peptide substrate from a tRNA molecule. Initially, arginylation was thought to occur only on N-terminally exposed acidic residues, and its function was thought to be limited to targeting proteins for degradation. However, more recent data have shown that ATE1 can arginylate side chains of internal acidic residues in a protein without necessarily affecting metabolic stability. This greatly expands the potential targets and functions of arginylation, but tools for studying this process have remained limited. Here, we report the first global screen specifically for side-chain arginylation. We generate and validate "pan-arginylation" antibodies, which are designed to detect side-chain arginylation in any amino acid sequence context. We use these antibodies for immunoaffinity enrichment of side-chain arginylated proteins from wildtype and Ate1 knockout cell lysates. In this way, we identify a limited set of proteins that likely undergo ATE1-dependent side-chain arginylation and that are enriched in specific cellular roles, including translation, splicing, and the cytoskeleton.
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Affiliation(s)
- Brittany MacTaggart
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marie Shimogawa
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marshall Lougee
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - E J Petersson
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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4
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Heo AJ, Kim SB, Kwon YT, Ji CH. The N-degron pathway: From basic science to therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194934. [PMID: 36990317 DOI: 10.1016/j.bbagrm.2023.194934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
The N-degron pathway is a degradative system in which single N-terminal (Nt) amino acids regulate the half-lives of proteins and other biological materials. These determinants, called N-degrons, are recognized by N-recognins that link them to the ubiquitin (Ub)-proteasome system (UPS) or autophagy-lysosome system (ALS). In the UPS, the Arg/N-degron pathway targets the Nt-arginine (Nt-Arg) and other N-degrons to assemble Lys48 (K48)-linked Ub chains by UBR box N-recognins for proteasomal proteolysis. In the ALS, Arg/N-degrons are recognized by the N-recognin p62/SQSTSM-1/Sequestosome-1 to induce cis-degradation of substrates and trans-degradation of various cargoes such as protein aggregates and subcellular organelles. This crosstalk between the UPS and ALP involves reprogramming of the Ub code. Eukaryotic cells developed diverse ways to target all 20 principal amino acids for degradation. Here we discuss the components, regulation, and functions of the N-degron pathways, with an emphasis on the basic mechanisms and therapeutic applications of Arg/N-degrons and N-recognins.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Su Bin Kim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea.
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea.
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5
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Abeywansha T, Huang W, Ye X, Nawrocki A, Lan X, Jankowsky E, Taylor DJ, Zhang Y. The structural basis of tRNA recognition by arginyl-tRNA-protein transferase. Nat Commun 2023; 14:2232. [PMID: 37076488 PMCID: PMC10115844 DOI: 10.1038/s41467-023-38004-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.
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Affiliation(s)
- Thilini Abeywansha
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xuan Ye
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Allison Nawrocki
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xin Lan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Derek J Taylor
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Yi Zhang
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Macedo-da-Silva J, Rosa-Fernandes L, Gomes VDM, Santiago VF, Santos DM, Molnar CMS, Barboza BR, de Souza EE, Marques RF, Boscardin SB, Durigon EL, Marinho CRF, Wrenger C, Marie SKN, Palmisano G. Protein Arginylation Is Regulated during SARS-CoV-2 Infection. Viruses 2023; 15:v15020290. [PMID: 36851505 PMCID: PMC9964439 DOI: 10.3390/v15020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In 2019, the world witnessed the onset of an unprecedented pandemic. By February 2022, the infection by SARS-CoV-2 has already been responsible for the death of more than 5 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER stress and activation of the unfolded protein response (UPR) pathway. Degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-degron pathway. RESULTS The role of protein arginylation during SARS-CoV-2 infection was elucidated. Protein arginylation was studied in Vero CCL-81, macrophage-like THP1, and Calu-3 cells infected at different times. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure levels of arginyl-tRNA-protein transferase (ATE1) and its substrates. Dysregulation of the N-degron pathway was specifically identified during coronavirus infections compared to other respiratory viruses. We demonstrated that during SARS-CoV-2 infection, there is an increase in ATE1 expression in Calu-3 and Vero CCL-81 cells. On the other hand, infected macrophages showed no enzyme regulation. ATE1 and protein arginylation was variant-dependent, as shown using P1 and P2 viral variants and HEK 293T cells transfection with the spike protein and receptor-binding domains (RBD). In addition, we report that ATE1 inhibitors, tannic acid and merbromine (MER) reduce viral load. This finding was confirmed in ATE1-silenced cells. CONCLUSIONS We demonstrate that ATE1 is increased during SARS-CoV-2 infection and its inhibition has potential therapeutic value.
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Affiliation(s)
- Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Vinicius de Morais Gomes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Deivid Martins Santos
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | | | - Bruno Rafael Barboza
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Rodolfo Ferreira Marques
- Laboratory of Antigen Targeting for Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Silvia Beatriz Boscardin
- Laboratory of Antigen Targeting for Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- School of Natural Sciences, Macquarie University, Sydney 2109, Australia
- Correspondence: or ; Tel.: +55-11-99920-8662
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7
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Galiano MR, Hallak ME. Assaying the Posttranslational Arginylation of Proteins in Cultured Cells. Methods Mol Biol 2023; 2620:51-61. [PMID: 37010748 DOI: 10.1007/978-1-0716-2942-0_7] [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
To evaluate the posttranslational arginylation of proteins in vivo, we describe a protocol for studying the 14C-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
- Dpt. Quimica Biologica Ranwel Caputto, Facultad de Ciencias Quimicas, Universidad Nacional de Córdoba, CIQUIBIC-CONICET, Córdoba, Argentina
| | - Marta E Hallak
- Dpt. Quimica Biologica Ranwel Caputto, Facultad de Ciencias Quimicas, Universidad Nacional de Córdoba, CIQUIBIC-CONICET, Córdoba, Argentina.
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8
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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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9
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Palandri A, Bonnet LV, Farias MG, Hallak ME, Galiano MR. Ablation of arginyl-tRNA-protein transferase in oligodendrocytes impairs central nervous system myelination. Glia 2021; 70:303-320. [PMID: 34669233 DOI: 10.1002/glia.24107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/08/2022]
Abstract
Addition of arginine (Arg) from tRNA can cause major alterations of structure and function of protein substrates. This post-translational modification, termed protein arginylation, is mediated by the enzyme arginyl-tRNA-protein transferase 1 (Ate1). Arginylation plays essential roles in a variety of cellular processes, including cell migration, apoptosis, and cytoskeletal organization. Ate1 is associated with neuronal functions such as neurogenesis and neurite growth. However, the role of Ate1 in glial development, including oligodendrocyte (OL) differentiation and myelination processes in the central nervous system, is poorly understood. The present study revealed a peak in Ate1 protein expression during myelination process in primary cultured OLs. Post-transcriptional downregulation of Ate1 reduced the number of OL processes, and branching complexity, in vitro. We conditionally ablated Ate1 from OLs in mice using 2',3'-cyclic nucleotide 3'-phosphodiesterase-Cre promoter ("Ate1-KO" mice), to assess the role of Ate1 in OL function and axonal myelination in vivo. Immunostaining for OL differentiation markers revealed a notable reduction of mature OLs in corpus callosum of 14-day-old Ate1-KO, but no changes in spinal cord, in comparison with wild-type controls. Local proliferation of OL precursor cells was elevated in corpus callosum of 21-day-old Ate1-KO, but was unchanged in spinal cord. Five-month-old Ate1-KO displayed reductions of mature OL number and myelin thickness, with alterations of motor behaviors. Our findings, taken together, demonstrate that Ate1 helps maintain proper OL differentiation and myelination in corpus callosum in vivo, and that protein arginylation plays an essential role in developmental myelination.
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Affiliation(s)
- Anabela Palandri
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
| | - Laura Vanesa Bonnet
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
| | - Maria Gimena Farias
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
| | - Marta Elena Hallak
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
| | - Mauricio Raul Galiano
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CIQUIBIC, Córdoba, Argentina
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10
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Kishimoto N, Okano R, Akita A, Miura S, Irie A, Takamune N, Misumi S. Arginyl-tRNA-protein transferase 1 contributes to governing optimal stability of the human immunodeficiency virus type 1 core. Retrovirology 2021; 18:30. [PMID: 34565409 PMCID: PMC8474785 DOI: 10.1186/s12977-021-00574-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/12/2021] [Indexed: 11/15/2022] Open
Abstract
Background The genome of human immunodeficiency virus type 1 (HIV-1) is encapsulated in a core consisting of viral capsid proteins (CA). After viral entry, the HIV-1 core dissociates and releases the viral genome into the target cell, this process is called uncoating. Uncoating of HIV-1 core is one of the critical events in viral replication and several studies show that host proteins positively or negatively regulate this process by interacting directly with the HIV-1 CA. Results Here, we show that arginyl-tRNA-protein transferase 1 (ATE1) plays an important role in the uncoating process by governing the optimal core stability. Yeast two-hybrid screening of a human cDNA library identified ATE1 as an HIV-1-CA-interacting protein and direct interaction of ATE1 with Pr55gag and p160gag − pol via HIV-1 CA was observed by cell-based pull-down assay. ATE1 knockdown in HIV-1 producer cells resulted in the production of less infectious viruses, which have normal amounts of the early products of the reverse transcription reaction but reduced amounts of the late products of the reverse transcription. Interestingly, ATE1 overexpression in HIV-1 producer cells also resulted in the production of poor infectious viruses. Cell-based fate-of-capsid assay, a commonly used method for evaluating uncoating by measuring core stability, showed that the amounts of pelletable cores in cells infected with the virus produced from ATE1-knockdown cells increased compared with those detected in the cells infected with the control virus. In contrast, the amounts of pelletable cores in cells infected with the virus produced from ATE1-overexpressing cells decreased compared with those detected in the cells infected with the control virus. Conclusions These results indicate that ATE1 expression levels in HIV-1 producer cells contribute to the adequate formation of a stable HIV-1 core. These findings provide insights into a novel mechanism of HIV-1 uncoating and revealed ATE1 as a new host factor regulating HIV-1 replication. Graphic abstract ![]()
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Affiliation(s)
- Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Ryosuke Okano
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Ayano Akita
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Satoshi Miura
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Ayaka Irie
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Nobutoki Takamune
- Kumamoto Innovative Development Organization, Kumamoto University, Kumamoto, 860- 8555, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan.
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Van V, Smith AT. ATE1-Mediated Post-Translational Arginylation Is an Essential Regulator of Eukaryotic Cellular Homeostasis. ACS Chem Biol 2020; 15:3073-3085. [PMID: 33228359 DOI: 10.1021/acschembio.0c00677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Arginylation is a protein post-translational modification catalyzed by arginyl-tRNA transferases (ATE1s), which are critical enzymes conserved across all eukaryotes. Arginylation is a key step in the Arg N-degron pathway, a hierarchical cellular signaling pathway that links the ubiquitin-dependent degradation of a protein to the identity of its N-terminal amino acid side chain. The fidelity of ATE1-catalyzed arginylation is imperative, as this post-translational modification regulates several essential biological processes such as cardiovascular maturation, chromosomal segregation, and even the stress response. While the process of ATE1-catalyzed arginylation has been studied in detail at the cellular level, much remains unknown about the structure of this important enzyme, its mechanism of action, and its regulation. In this work, we detail the current state of knowledge on ATE1-catalyzed arginylation, and we discuss both ongoing and future directions that will reveal the structural and mechanistic details of this essential eukaryotic cellular regulator.
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Affiliation(s)
- Verna Van
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Aaron T. Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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12
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Heat stress induced arginylation of HuR promotes alternative polyadenylation of Hsp70.3 by regulating HuR stability and RNA binding. Cell Death Differ 2020; 28:730-747. [PMID: 32929216 DOI: 10.1038/s41418-020-00619-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/08/2022] Open
Abstract
Arginylation was previously found to promote stabilization of heat shock protein 70.3 (Hsp70.3) mRNA and cell survival in mouse embryonic fibroblasts (MEFs) on exposure to heat stress (HS). In search of a factor responsible for these phenomena, the current study identified human antigen R (HuR) as a direct target of arginylation. HS induced arginylation of HuR affected its stability and RNA binding activity. Arginylated HuR failed to bind Hsp70.3 3' UTR, allowing the recruitment of cleavage stimulating factor 64 (CstF64) in the proximal poly-A-site (PAS), generating transcripts with short 3'UTR. However, HuR from Ate1 knock out (KO) MEFs bound to proximal PAS region with higher affinity, thus excluded CstF64 recruitment. This inhibited the alternative polyadenylation (APA) of Hsp70.3 mRNA and generated the unstable transcripts with long 3'UTR. The inhibition of RNA binding activity of HuR was traced to arginylation-coupled phosphorylation of HuR, by check point kinase 2 (Chk2). Arginylation of HuR occurred at the residue D15 and the arginylation was needed for the phosphorylation. Accumulation of HuR also decreased cell viability upon HS. In conclusion, arginylation dependent modifications of HuR maintained its cellular homeostasis, and promoted APA of Hsp70.3 pre-mRNA, during early HS response.
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13
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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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14
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Lassak J, Koller F, Krafczyk R, Volkwein W. Exceptionally versatile – arginine in bacterial post-translational protein modifications. Biol Chem 2019; 400:1397-1427. [DOI: 10.1515/hsz-2019-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/01/2019] [Indexed: 12/24/2022]
Abstract
Abstract
Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Franziska Koller
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Wolfram Volkwein
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
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15
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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16
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Singh A, Borah AK, Deka K, Gogoi AP, Verma K, Barah P, Saha S. Arginylation regulates adipogenesis by regulating expression of PPARγ at transcript and protein level. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:596-607. [DOI: 10.1016/j.bbalip.2018.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/28/2022]
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17
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Metabolite sensing and signaling in cell metabolism. Signal Transduct Target Ther 2018; 3:30. [PMID: 30416760 PMCID: PMC6224561 DOI: 10.1038/s41392-018-0024-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 02/07/2023] Open
Abstract
Metabolite sensing is one of the most fundamental biological processes. During evolution, multilayered mechanisms developed to sense fluctuations in a wide spectrum of metabolites, including nutrients, to coordinate cellular metabolism and biological networks. To date, AMPK and mTOR signaling are among the best-understood metabolite-sensing and signaling pathways. Here, we propose a sensor-transducer-effector model to describe known mechanisms of metabolite sensing and signaling. We define a metabolite sensor by its specificity, dynamicity, and functionality. We group the actions of metabolite sensing into three different modes: metabolite sensor-mediated signaling, metabolite-sensing module, and sensing by conjugating. With these modes of action, we provide a systematic view of how cells sense sugars, lipids, amino acids, and metabolic intermediates. In the future perspective, we suggest a systematic screen of metabolite-sensing macromolecules, high-throughput discovery of biomacromolecule-metabolite interactomes, and functional metabolomics to advance our knowledge of metabolite sensing and signaling. Most importantly, targeting metabolite sensing holds great promise in therapeutic intervention of metabolic diseases and in improving healthy aging. A simple, three-part model provides a systematic view of how cells sense sugars, lipids, amino acids and metabolic intermediates. Cells quickly and accurately perceive changes in intra- and extracellular molecules such as nutrients to respond to changing environments. Drawing on existing knowledge about AMPK and MTORC1 signaling, Yi-Ping Wang and Qun-Ying Lei at Fudan University in Shanghai propose a model in which three components: a sensor, transducer and effector enable metabolic sensing and signaling to proceed. The sensor detects the metabolite, and, through conjugation, conformational changes or protein–protein interactions, transmits this information to the transducer, which decides the appropriate response. The transducer then issues orders to effector proteins which coordinate the action. The future identification of novel metabolic sensors through systematic screening could lead to new therapeutic interventions for metabolic and age-related diseases.
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18
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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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19
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Plant cysteine oxidases are dioxygenases that directly enable arginyl transferase-catalysed arginylation of N-end rule targets. Nat Commun 2017; 8:14690. [PMID: 28332493 PMCID: PMC5376641 DOI: 10.1038/ncomms14690] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/20/2017] [Indexed: 02/06/2023] Open
Abstract
Crop yield loss due to flooding is a threat to food security. Submergence-induced hypoxia in plants results in stabilization of group VII ETHYLENE RESPONSE FACTORs (ERF-VIIs), which aid survival under these adverse conditions. ERF-VII stability is controlled by the N-end rule pathway, which proposes that ERF-VII N-terminal cysteine oxidation in normoxia enables arginylation followed by proteasomal degradation. The PLANT CYSTEINE OXIDASEs (PCOs) have been identified as catalysts of this oxidation. ERF-VII stabilization in hypoxia presumably arises from reduced PCO activity. We directly demonstrate that PCO dioxygenase activity produces Cys-sulfinic acid at the N terminus of an ERF-VII peptide, which then undergoes efficient arginylation by an arginyl transferase (ATE1). This provides molecular evidence of N-terminal Cys-sulfinic acid formation and arginylation by N-end rule pathway components, and a substrate of ATE1 in plants. The PCOs and ATE1 may be viable intervention targets to stabilize N-end rule substrates, including ERF-VIIs, to enhance submergence tolerance in agriculture. The N-end rule pathway targets substrate proteins for proteasomal degradation. Here, White et al. show that Arabidopsis PLANT CYSTEINE OXIDASEs show dioxygenase activity producing Cys-sulfinic acid at the N-terminus of target proteins, which then act as direct substrates for arginyl transferase.
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20
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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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21
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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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22
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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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23
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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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24
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Fung AWS, Payoe R, Fahlman RP. Perspectives and Insights into the Competition for Aminoacyl-tRNAs between the Translational Machinery and for tRNA Dependent Non-Ribosomal Peptide Bond Formation. Life (Basel) 2015; 6:life6010002. [PMID: 26729173 PMCID: PMC4810233 DOI: 10.3390/life6010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/23/2015] [Accepted: 12/25/2015] [Indexed: 12/19/2022] Open
Abstract
Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is the sole member of this class of enzyme found in Escherichia coli and catalyzes the transfer of leucine to the N-termini of proteins which result in the targeted degradation of the modified protein. Recent investigations on the tRNA specificity of L/F-transferase have revealed the unique recognition nucleotides for a preferred Leu-tRNALeu isoacceptor substrate. In addition to discussing this tRNA selectivity by L/F-transferase, we present and discuss a hypothesis and its implications regarding the apparent competition for this aminoacyl-tRNA between L/F-transferase and the translational machinery. Our discussion reveals a hypothetical involvement of the bacterial stringent response that occurs upon amino acid limitation as a potential cellular event that may reduce this competition and provide the opportunity for L/F-transferase to readily increase its access to the pool of aminoacylated tRNA substrates.
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Affiliation(s)
- Angela W S Fung
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada.
| | - Roshani Payoe
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Institute of Technology, Faculty of Science and Technology, University of Tartu, Noorse St 1, Tartu 50411, Estonia.
| | - Richard P Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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25
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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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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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Quistgaard EM, Grøftehauge MK, Madsen P, Pallesen LT, Christensen B, Sørensen ES, Nissen P, Petersen CM, Thirup SS. Revisiting the structure of the Vps10 domain of human sortilin and its interaction with neurotensin. Protein Sci 2014; 23:1291-300. [PMID: 24985322 DOI: 10.1002/pro.2512] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/17/2014] [Accepted: 06/26/2014] [Indexed: 12/16/2022]
Abstract
Sortilin is a multifunctional receptor involved in sorting and apoptosis. We have previously reported a 2.0-Å structure of the Vps10 ectodomain in complex with one of its ligands, the tridecapeptide neurotensin. Here we set out to further characterize the structural properties of sortilin and its interaction with neurotensin. To this end, we have determined a new 2.7 Å structure using a crystal grown with a 10-fold increased concentration of neurotensin. Here a second peptide fragment was observed within the Vps10 β-propeller, which may in principle either represent a second molecule of neurotensin or the N-terminal part of the molecule bound at the previously identified binding site. However, in vitro binding experiments strongly favor the latter hypothesis. Neurotensin thus appears to bind with a 1:1 stoichiometry, and whereas the N-terminus does not bind on its own, it enhances the affinity in context of full-length neurotensin. We conclude that the N-terminus of neurotensin probably functions as an affinity enhancer for binding to sortilin by engaging the second binding site. Crystal packing differs partly from the previous structure, which may be due to variations in the degree and pattern of glycosylations. Consequently, a notable hydrophobic loop, not modeled previously, could now be traced. A computational analysis suggests that this and a neighboring loop may insert into the membrane and thus restrain movement of the Vps10 domain. We have, furthermore, mapped all N-linked glycosylations of CHO-expressed human sortilin by mass spectrometry and find that their locations are compatible with membrane insertion of the hydrophobic loops.
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Affiliation(s)
- Esben M Quistgaard
- Department of Molecular Biology and Genetics, MIND Centre, Aarhus University, Gustav Wieds Vej 10C, DK 8000, Aarhus C, Denmark; Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177, Stockholm, Sweden
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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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Varshavsky A. The N-end rule pathway and regulation by proteolysis. Protein Sci 2011; 20:1298-345. [PMID: 21633985 PMCID: PMC3189519 DOI: 10.1002/pro.666] [Citation(s) in RCA: 524] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 05/16/2011] [Accepted: 05/18/2011] [Indexed: 01/12/2023]
Abstract
The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. Degradation signals (degrons) that are targeted by the N-end rule pathway include a set called N-degrons. The main determinant of an N-degron is a destabilizing N-terminal residue of a protein. In eukaryotes, the N-end rule pathway is a part of the ubiquitin system and consists of two branches, the Ac/N-end rule and the Arg/N-end rule pathways. The Ac/N-end rule pathway targets proteins containing N(α) -terminally acetylated (Nt-acetylated) residues. The Arg/N-end rule pathway recognizes unacetylated N-terminal residues and involves N-terminal arginylation. Together, these branches target for degradation a majority of cellular proteins. For example, more than 80% of human proteins are cotranslationally Nt-acetylated. Thus most proteins harbor a specific degradation signal, termed (Ac)N-degron, from the moment of their birth. Specific N-end rule pathways are also present in prokaryotes and in mitochondria. Enzymes that produce N-degrons include methionine-aminopeptidases, caspases, calpains, Nt-acetylases, Nt-amidases, arginyl-transferases and leucyl-transferases. Regulated degradation of specific proteins by the N-end rule pathway mediates a legion of physiological functions, including the sensing of heme, oxygen, and nitric oxide; selective elimination of misfolded proteins; the regulation of DNA repair, segregation and condensation; the signaling by G proteins; the regulation of peptide import, fat metabolism, viral and bacterial infections, apoptosis, meiosis, spermatogenesis, neurogenesis, and cardiovascular development; and the functioning of adult organs, including the pancreas and the brain. Discovered 25 years ago, this pathway continues to be a fount of biological insights.
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Affiliation(s)
- Alexander Varshavsky
- 1Division of Biology, California Institute of Technology, Pasadena, California 91125.
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Posttranslational arginylation as a global biological regulator. Dev Biol 2011; 358:1-8. [PMID: 21784066 DOI: 10.1016/j.ydbio.2011.06.043] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/08/2011] [Accepted: 06/29/2011] [Indexed: 02/03/2023]
Abstract
Posttranslational modifications constitute a major field of emerging biological significance as mounting evidence demonstrates their key role in multiple physiological processes. Following in the footsteps of protein phosphorylation studies, new modifications are being shown to regulate protein properties and functions in vivo. Among such modifications, an important role belongs to protein arginylation - posttranslational tRNA-mediated addition of arginine, to proteins by arginyltransferase, ATE1. Recent studies show that arginylation is essential for embryogenesis in many organisms and that it regulates such important processes as heart development, angiogenesis, and tissue morphogenesis in mammals. This review summarizes the key data in the protein arginylation field since its original discovery to date.
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Arginyltransferase is an ATP-independent self-regulating enzyme that forms distinct functional complexes in vivo. ACTA ACUST UNITED AC 2011; 18:121-30. [PMID: 21276945 DOI: 10.1016/j.chembiol.2010.10.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 10/11/2010] [Accepted: 10/25/2010] [Indexed: 11/21/2022]
Abstract
Posttranslational arginylation mediated by arginyl transferase (ATE1) plays an important role in cardiovascular development, cell motility, and regulation of cytoskeleton and metabolic enzymes. This protein modification was discovered decades ago, however, the arginylation reaction and the functioning of ATE1 remained poorly understood because of the lack of good biochemical models. Here, we report the development of an in vitro arginylation system, in which ATE1 function and molecular requirements can be tested using purified recombinant ATE1 isoforms supplemented with a controlled number of components. Our results show that arginylation reaction is a self-sufficient, ATP-independent process that can affect different sites in a polypeptide and that arginyl transferases form different molecular complexes in vivo, associate with components of the translation machinery, and have distinct, partially overlapping subsets of substrates, suggesting that these enzymes play different physiological functions.
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Rubio-Zapata HA, Rembao-Bojorquez JD, Arango-Rodriguez ML, Dupouy S, Forgez P, Martinez-Fong D. NT-polyplex: a new tool for therapeutic gene delivery to neuroblastoma tumors. Cancer Gene Ther 2009; 16:573-84. [PMID: 19180142 DOI: 10.1038/cgt.2009.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Neurotensin (NT)-polyplex is a nonviral system for the targeted gene delivery to cells that express and internalize the high-affinity NT receptor (NTSR1). In hemiparkinsonian rats, we previously demonstrated the morphological and functional recovery from dopaminergic neurodegeneration using the NT-polyplex as a vehicle to transfect a neurotrophic gene. The main objective of this work was to demonstrate the feasibility of NT-polyplex to transfect reporter or therapeutic genes into neuroblastoma tumors through the blood stream or by intratumoral injection. N1E-115 cells known to express NTSR1 were allografted into athymic mice to generate the neuroblastoma tumor model. Both routes of administration allowed the NT-polyplex to reach and transfect tumoral cells. A low transgene expression was also detected in intestinal tract cells only after the injection into the blood stream. The transfection of the thymidine kinase (HSVTK) suicide gene followed by ganciclovir (GCV) treatment decreased the size and weight of neuroblastoma tumors by 30-50% and increased apoptosis compared to controls. This study shows the potential of the NT-polyplex as specific gene-transfer system for NTSR1 cancer cells.
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Affiliation(s)
- H A Rubio-Zapata
- Department of Physiology, Biophysics and Neuroscience, CINVESTAV, Mexico DF, Mexico
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Rai R, Wong CCL, Xu T, Leu NA, Dong DW, Guo C, McLaughlin KJ, Yates JR, Kashina A. Arginyltransferase regulates alpha cardiac actin function, myofibril formation and contractility during heart development. Development 2008; 135:3881-9. [PMID: 18948421 DOI: 10.1242/dev.022723] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Post-translational arginylation mediated by arginyltransferase (Ate1) is essential for cardiovascular development and angiogenesis in mammals and directly affects myocardium structure in the developing heart. We recently showed that arginylation exerts a number of intracellular effects by modifying proteins involved in the functioning of the actin cytoskeleton and in cell motility. Here, we investigated the role of arginylation in the development and function of cardiac myocytes and their actin-containing structures during embryogenesis. Biochemical and mass spectrometry analyses showed that alpha cardiac actin undergoes arginylation at four sites during development. Ultrastructural analysis of the myofibrils in wild-type and Ate1 knockout mouse hearts showed that the absence of arginylation results in defects in myofibril structure that delay their development and affect the continuity of myofibrils throughout the heart, predicting defects in cardiac contractility. Comparison of cardiac myocytes derived from wild-type and Ate1 knockout mouse embryos revealed that the absence of arginylation results in abnormal beating patterns. Our results demonstrate cell-autonomous cardiac myocyte defects in arginylation knockout mice that lead to severe congenital abnormalities similar to those observed in human disease, and outline a new function of arginylation in the regulation of the actin cytoskeleton in cardiac myocytes.
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Affiliation(s)
- Reena Rai
- Department of Animal Biology and School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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34
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Wong CCL, Xu T, Rai R, Bailey AO, Yates JR, Wolf YI, Zebroski H, Kashina A. Global analysis of posttranslational protein arginylation. PLoS Biol 2007; 5:e258. [PMID: 17896865 PMCID: PMC1988855 DOI: 10.1371/journal.pbio.0050258] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 07/30/2007] [Indexed: 11/27/2022] Open
Abstract
Posttranslational arginylation is critical for embryogenesis, cardiovascular development, and angiogenesis, but its molecular effects and the identity of proteins arginylated in vivo are largely unknown. Here we report a global analysis of this modification on the protein level and identification of 43 proteins arginylated in vivo on highly specific sites. Our data demonstrate that unlike previously believed, arginylation can occur on any N-terminally exposed residue likely defined by a structural recognition motif on the protein surface, and that it preferentially affects a number of physiological systems, including cytoskeleton and primary metabolic pathways. The results of our study suggest that protein arginylation is a general mechanism for regulation of protein structure and function and outline the potential role of protein arginylation in cell metabolism and embryonic development. A common cellular mechanism for the regulation of proteins, once they have been translated from mRNA, is the addition and removal of chemical groups via enzymatic reactions. The posttranslational addition of arginyl groups is critical for the embryonic development and survival of an organism, but the molecular effects and the identity of proteins arginylated in vivo are largely unknown. We developed a technique to screen large numbers of proteins for this modification and identified 43 proteins arginylated in vivo on highly specific sites. Arginylation can occur on any exposed residue at the N-terminus of a protein and appears to require a specific structural recognition motif on the protein surface. It preferentially affects a number of physiological systems, including cytoskeleton and primary metabolic pathways and seems to be a general mechanism for regulation of protein structure and function. Our data provide insights into the previously unknown arginylation-dependent mechanisms of the regulation of embryonic development. A comprehensive study indicates that protein arginylation may be a general mechanism for regulation of protein structure and function, similar to other major posttranslational modifications.
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Affiliation(s)
- Catherine C. L Wong
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Tao Xu
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Reena Rai
- Department of Animal Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aaron O Bailey
- The Scripps Research Institute, LaJolla, California, United States of America
| | - John R Yates
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Henry Zebroski
- Rockefeller University, New York, NewYork, United States of America
| | - Anna Kashina
- Department of Animal Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * To whom correspondence should be addressed. E-mail:
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35
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Tasaki T, Kwon YT. The mammalian N-end rule pathway: new insights into its components and physiological roles. Trends Biochem Sci 2007; 32:520-8. [PMID: 17962019 DOI: 10.1016/j.tibs.2007.08.010] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 08/21/2007] [Accepted: 08/21/2007] [Indexed: 12/30/2022]
Abstract
The N-end rule pathway is a ubiquitin-dependent proteolytic system, in which destabilizing N-terminal residues of short-lived proteins function as an essential determinant of an N-terminal degradation signal (N-degron). An N-degron can be created from a pre-N-degron through specific N-terminal modifications, providing a means conditionally to destabilize otherwise stable polypeptides. The pathway has been found in all organisms examined, from prokaryotes to eukaryotes. Recent biochemical and proteomic studies identified many components of the mammalian N-end rule pathway, including a family of substrate recognition ubiquitin ligases and their substrates. The genetic dissection in animals and humans revealed its essential role in various vital physiological processes, ranging from cardiovascular development and meiosis to the pathogenesis of human genetic diseases. These discoveries have provided new insights into the components, functions and mechanics of this unique proteolytic system.
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Affiliation(s)
- Takafumi Tasaki
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
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