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Mughal AA, Grieg Z, Skjellegrind H, Fayzullin A, Lamkhannat M, Joel M, Ahmed MS, Murrell W, Vik-Mo EO, Langmoen IA, Stangeland B. Knockdown of NAT12/NAA30 reduces tumorigenic features of glioblastoma-initiating cells. Mol Cancer 2015; 14:160. [PMID: 26292663 PMCID: PMC4546247 DOI: 10.1186/s12943-015-0432-z] [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: 10/28/2014] [Accepted: 08/12/2015] [Indexed: 01/21/2023] Open
Abstract
Background Glioblastoma (GBM) is the most common primary brain malignancy and confers a dismal prognosis. GBMs harbor glioblastoma-initiating cells (GICs) that drive tumorigenesis and contribute to therapeutic resistance and tumor recurrence. Consequently, there is a strong rationale to target this cell population in order to develop new molecular therapies against GBM. Accumulating evidence indicates that Nα-terminal acetyltransferases (NATs), that are dysregulated in numerous human cancers, can serve as therapeutic targets. Methods Microarrays were used to study the expression of several NATs including NAT12/NAA30 in clinical samples and stem cell cultures. The expression of NAT12/NAA30 was analyzed using qPCR, immunolabeling and western blot. We conducted shRNA-mediated knockdown of NAT12/NAA30 gene in GICs and studied the effects on cell viability, sphere-formation and hypoxia sensitivity. Intracranial transplantation to SCID mice enabled us to investigate the effects of NAT12/NAA30 depletion in vivo. Using microarrays we identified genes and biochemical pathways whose expression was altered upon NAT12/NAA30 down-regulation. Results While decreased expression of the distal 3’UTR of NAT12/NAA30 was generally observed in GICs and GBMs, this gene was strongly up-regulated at the protein level in GBM and GICs. The increased protein levels were not caused by increased levels of the steady state mRNA but rather by other mechanisms. Also, shorter 3’UTR of NAT12/NAA30 correlated with poor survival in glioma patients. As well, we observed previously not described nuclear localization of this typically cytoplasmic protein. When compared to non-silencing controls, cells featuring NAT12/NAA30 knockdown exhibited reduced cell viability, sphere-forming ability, and mitochondrial hypoxia tolerance. Intracranial transplantation showed that knockdown of NAT12/NAA30 resulted in prolonged animal survival. Microarray analysis of the knockdown cultures showed reduced levels of HIF1α and altered expression of several other genes involved in the hypoxia response. Furthermore, NAT12/NAA30 knockdown correlated with expressional dysregulation of genes involved in the p53 pathway, ribosomal assembly and cell proliferation. Western blot analysis revealed reduction of HIF1α, phospho-MTOR(Ser2448) and higher levels of p53 and GFAP in these cultures. Conclusion NAT12/NAA30 plays an important role in growth and survival of GICs possibly by regulating hypoxia response (HIF1α), levels of p-MTOR (Ser2448) and the p53 pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0432-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Awais A Mughal
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway.
| | - Zanina Grieg
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Håvard Skjellegrind
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Artem Fayzullin
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Mustapha Lamkhannat
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Mrinal Joel
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway. .,Laboratory of Neural Development and Optical Recording (NDEVOR), Department of Physiology, Institute of Basic Medical Sciences University of Oslo, Oslo, Norway.
| | - M Shakil Ahmed
- Institute for Surgical Research, Oslo University Hospital and Center for Heart Failure Research, University of Oslo, Oslo, Norway.
| | - Wayne Murrell
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Einar O Vik-Mo
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Iver A Langmoen
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Biljana Stangeland
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway.
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102
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The N-terminal acetyltransferase Naa10 is essential for zebrafish development. Biosci Rep 2015; 35:BSR20150168. [PMID: 26251455 PMCID: PMC4613686 DOI: 10.1042/bsr20150168] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 06/30/2015] [Indexed: 11/17/2022] Open
Abstract
The Naa10 (Nα acetyltransferase 10) N-terminal acetyltransferase is implicated in cancer and developmental syndromes in humans. We show that its enzymatic activity is conserved in zebrafish, and that Naa10 depletion leads to developmental abnormalities. N-terminal acetylation, catalysed by N-terminal acetyltransferases (NATs), is among the most common protein modifications in eukaryotes and involves the transfer of an acetyl group from acetyl-CoA to the α-amino group of the first amino acid. Functions of N-terminal acetylation include protein degradation and sub-cellular targeting. Recent findings in humans indicate that a dysfunctional Nα-acetyltransferase (Naa) 10, the catalytic subunit of NatA, the major NAT, is associated with lethality during infancy. In the present study, we identified the Danio rerio orthologue zebrafish Naa 10 (zNaa10). In vitro N-terminal acetylation assays revealed that zNaa10 has NAT activity with substrate specificity highly similar to that of human Naa10. Spatiotemporal expression pattern was determined by in situ hybridization, showing ubiquitous expression with especially strong staining in brain and eye. By morpholino-mediated knockdown, we demonstrated that naa10 morphants displayed increased lethality, growth retardation and developmental abnormalities like bent axis, abnormal eyes and bent tails. In conclusion, we identified the zebrafish Naa10 orthologue and revealed that it is essential for normal development and viability of zebrafish.
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103
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Ho N, Gendron RL, Grozinger K, Whelan MA, Hicks EA, Tennakoon B, Gardiner D, Good WV, Paradis H. Tubedown regulation of retinal endothelial permeability signaling pathways. Biol Open 2015; 4:970-9. [PMID: 26142315 PMCID: PMC4542279 DOI: 10.1242/bio.010496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tubedown (Tbdn; Naa15), a subunit of the N-terminal acetyltransferase NatA, complexes with the c-Src substrate Cortactin and supports adult retinal homeostasis through regulation of vascular permeability. Here we investigate the role of Tbdn expression on signaling components of retinal endothelial permeability to understand how Tbdn regulates the vasculature and supports retinal homeostasis. Tbdn knockdown-induced hyperpermeability to Albumin in retinal endothelial cells was associated with an increase in the levels of activation of the Src family kinases (SFK) c-Src, Fyn and Lyn and phospho-Cortactin (Tyr421). The knockdown of Cortactin expression reduced Tbdn knockdown-induced permeability to Albumin and the levels of activated SFK. Inhibition of SFK in retinal endothelial cells decreased Tbdn knockdown-induced permeability to Albumin and phospho-Cortactin (Tyr421) levels. Retinal lesions of endothelial-specific Tbdn knockdown mice, with tissue thickening, fibrovascular growth, and hyperpermeable vessels displayed an increase in the levels of activated c-Src. Moreover, the retinal lesions of patients with proliferative diabetic retinopathy (PDR) associated with a loss of Tbdn expression and hyperpermeability to Albumin displayed increased levels of activated SFK in retinal blood vessels. Taken together, these results implicate Tbdn as an important regulator of retinal endothelial permeability and homeostasis by modulating a signaling pathway involving c-Src and Cortactin.
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Affiliation(s)
- Nhu Ho
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - Robert L Gendron
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - Kindra Grozinger
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - Maria A Whelan
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - Emily Anne Hicks
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - Bimal Tennakoon
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - Danielle Gardiner
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
| | - William V Good
- Smith-Kettlewell Eye Research Institute, San Francisco, CA 94115, USA
| | - Hélène Paradis
- Division of BioMedical Sciences, Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3V6
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104
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Giglione C, Fieulaine S, Meinnel T. N-terminal protein modifications: Bringing back into play the ribosome. Biochimie 2015; 114:134-46. [PMID: 25450248 DOI: 10.1016/j.biochi.2014.11.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
N-terminal protein modifications correspond to the first modifications which in principle any protein may undergo, before translation is completed by the ribosome. This class of essential modifications can have different nature or function and be catalyzed by a variety of dedicated enzymes. Here, we review the current state of the major N-terminal co-translational modifications, with a particular emphasis to their catalysts, which belong to metalloprotease and acyltransferase clans. The earliest of these modifications corresponds to the N-terminal methionine excision, an ubiquitous and essential process leading to the removal of the first methionine. N-alpha acetylation occurs also in all Kingdoms although its extent appears to be significantly increased in higher eukaryotes. Finally, N-myristoylation is a crucial pathway existing only in eukaryotes. Recent studies dealing on how some of these co-translational modifiers might work in close vicinity of the ribosome is starting to provide new information on when these modifications exactly take place on the elongating nascent chain and the interplay with other ribosome biogenesis factors taking in charge the nascent chains. Here a comprehensive overview of the recent advances in the field of N-terminal protein modifications is given.
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Affiliation(s)
- Carmela Giglione
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
| | - Sonia Fieulaine
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
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105
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Varland S, Osberg C, Arnesen T. N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects. Proteomics 2015; 15:2385-401. [PMID: 25914051 PMCID: PMC4692089 DOI: 10.1002/pmic.201400619] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/04/2015] [Accepted: 04/21/2015] [Indexed: 01/18/2023]
Abstract
The vast majority of eukaryotic proteins are N-terminally modified by one or more processing enzymes. Enzymes acting on the very first amino acid of a polypeptide include different peptidases, transferases, and ligases. Methionine aminopeptidases excise the initiator methionine leaving the nascent polypeptide with a newly exposed amino acid that may be further modified. N-terminal acetyl-, methyl-, myristoyl-, and palmitoyltransferases may attach an acetyl, methyl, myristoyl, or palmitoyl group, respectively, to the α-amino group of the target protein N-terminus. With the action of ubiquitin ligases, one or several ubiquitin molecules are transferred, and hence, constitute the N-terminal modification. Modifications at protein N-termini represent an important contribution to proteomic diversity and complexity, and are essential for protein regulation and cellular signaling. Consequently, dysregulation of the N-terminal modifying enzymes is implicated in human diseases. We here review the different protein N-terminal modifications occurring co- or post-translationally with emphasis on the responsible enzymes and their substrate specificities.
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Affiliation(s)
- Sylvia Varland
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Camilla Osberg
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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106
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Lai ZW, Gomez-Auli A, Keller EJ, Mayer B, Biniossek ML, Schilling O. Enrichment of protein N-termini by charge reversal of internal peptides. Proteomics 2015; 15:2470-8. [DOI: 10.1002/pmic.201500023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/01/2015] [Accepted: 05/21/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Zon W. Lai
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Alejandro Gomez-Auli
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Faculty of Biology; University of Freiburg; Freiburg Germany
- Spemann Graduate School of Biology and Medicine; University of Freiburg; Freiburg Germany
| | - Eva J. Keller
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Bettina Mayer
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Martin L. Biniossek
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Spemann Graduate School of Biology and Medicine; University of Freiburg; Freiburg Germany
- BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg Germany
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107
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Silva RD, Martinho RG. Developmental roles of protein N-terminal acetylation. Proteomics 2015; 15:2402-9. [PMID: 25920796 DOI: 10.1002/pmic.201400631] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/26/2015] [Accepted: 04/24/2015] [Indexed: 12/30/2022]
Abstract
Discovered more than 50 years ago, N-terminal acetylation (N-Ac) is one of the most common protein modifications. Catalyzed by different N-terminal acetyltransferases (NATs), N-Ac was originally believed to mostly promote protein stability. However, several functional consequences at substrate level were recently described that yielded important new insights about the distinct molecular functions for this modification. The ubiquitous and apparent irreversible nature of this protein modification leads to the assumption that N-Ac mostly executes constitutive functions. In spite of the large number of substrates for each NAT, recent studies in multicellular organisms have nevertheless indicated very specific phenotypes after NAT loss. This raises the hypothesis that in vivo N-Ac is only functionally rate limiting for a small subset of substrates. In this review, we will discuss the function of N-Ac in the context of a developing organism. We will propose that some rate limiting NAT substrates may be tissue-specific leading to differential functions of N-Ac during development of multicellular organisms. Moreover, we will also propose the existence of tissue and developmental-specific mechanisms that differentially regulate N-Ac.
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Affiliation(s)
- Rui D Silva
- Departamento de Ciências Biomédicas e Medicina, and Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Rui G Martinho
- Departamento de Ciências Biomédicas e Medicina, and Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, Faro, Portugal.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
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108
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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109
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Magin RS, Liszczak GP, Marmorstein R. The molecular basis for histone H4- and H2A-specific amino-terminal acetylation by NatD. Structure 2015; 23:332-41. [PMID: 25619998 DOI: 10.1016/j.str.2014.10.025] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022]
Abstract
N-terminal acetylation is among the most common protein modifications in eukaryotes and is mediated by evolutionarily conserved N-terminal acetyltransferases (NATs). NatD is among the most selective NATs; its only known substrates are histones H4 and H2A, containing the N-terminal sequence SGRGK in humans. Here we characterize the molecular basis for substrate-specific acetylation by NatD by reporting its crystal structure bound to cognate substrates and performing related biochemical studies. A novel N-terminal segment wraps around the catalytic core domain to make stabilizing interactions, and the α1-α2 and β6-β7 loops adopt novel conformations to properly orient the histone N termini in the binding site. Ser1 and Arg3 of the histone make extensive contacts to highly conserved NatD residues in the substrate binding pocket, and flanking glycine residues also appear to contribute to substrate-specific binding by NatD, together defining a Ser-Gly-Arg-Gly recognition sequence. These studies have implications for understanding substrate-specific acetylation by NAT enzymes.
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Affiliation(s)
- Robert S Magin
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glen P Liszczak
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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110
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Molecular, Cellular, and Physiological Significance of N-Terminal Acetylation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 316:267-305. [DOI: 10.1016/bs.ircmb.2015.01.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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111
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Myklebust LM, Van Damme P, Støve SI, Dörfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Hum Mol Genet 2014; 24:1956-76. [PMID: 25489052 PMCID: PMC4355026 DOI: 10.1093/hmg/ddu611] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The X-linked lethal Ogden syndrome was the first reported human genetic disorder associated with a mutation in an N-terminal acetyltransferase (NAT) gene. The affected males harbor an Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of NatA, the major human NAT involved in the co-translational acetylation of proteins. Structural models and molecular dynamics simulations of the human NatA and its S37P mutant highlight differences in regions involved in catalysis and at the interface between Naa10 and the auxiliary subunit hNaa15. Biochemical data further demonstrate a reduced catalytic capacity and an impaired interaction between hNaa10 S37P and Naa15 as well as Naa50 (NatE), another interactor of the NatA complex. N-Terminal acetylome analyses revealed a decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells, supporting the genetic findings and our hypothesis regarding reduced Nt-acetylation of a subset of NatA/NatE-type substrates as one etiology for Ogden syndrome. Furthermore, Ogden syndrome fibroblasts display abnormal cell migration and proliferation capacity, possibly linked to a perturbed retinoblastoma pathway. N-Terminal acetylation clearly plays a role in Ogden syndrome, thus revealing the in vivo importance of N-terminal acetylation in human physiology and disease.
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Affiliation(s)
- Line M Myklebust
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium,
| | - Svein I Støve
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Max J Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA
| | - Angèle Abboud
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Thomas V Kalvik
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Cedric Grauffel
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Veronique Jonckheere
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Hanna Kaasa
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Glen Liszczak
- Program in Gene Expression and Regulation, Wistar Institute, PA 19104, USA, Department of Chemistry, and Department of Biochemistry and Biophysics and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, PA 19104, USA, Department of Chemistry, and Department of Biochemistry and Biophysics and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA,
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway,
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112
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SEO JIHAE, PARK JIHYEON, LEE EUNJI, KIM KYUWON. Different subcellular localizations and functions of human ARD1 variants. Int J Oncol 2014; 46:701-7. [DOI: 10.3892/ijo.2014.2770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/11/2014] [Indexed: 11/05/2022] Open
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113
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Arrest defective 1 regulates the oxidative stress response in human cells and mice by acetylating methionine sulfoxide reductase A. Cell Death Dis 2014; 5:e1490. [PMID: 25341044 PMCID: PMC4649535 DOI: 10.1038/cddis.2014.456] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/03/2014] [Accepted: 09/15/2014] [Indexed: 12/27/2022]
Abstract
Methionine sulfoxide reductase A (MSRA) protects proteins from oxidation, and also helps remove reactive oxygen species (ROS) by recovering antioxidant enzymes inactivated by oxidation. Although its functions have been investigated extensively, little is known about the mechanism by which MSRA is regulated. Arrest defective 1 (ARD1) is an enzyme that catalyzes not only N-terminal acetylation as a cotranslational modification but also lysine acetylation as a posttranslational modification. ARD1, which is expressed in most cell types, is believed to participate in diverse biological processes, but its roles are poorly understood. Given that MSRA was hunted in a yeast two-hybrid screen with ARD1 as the bait, we here investigated whether ARD1 is a novel regulator of MSRA. ARD1 was shown to interact with and acetylate MSRA in both cells and test tubes. It specifically acetylated the K49 residue of MSRA, and by doing so repressed the enzymatic function of MSRA. ARD1 increased cellular levels of ROS, carbonylated proteins and DNA breaks under oxidative stress. Moreover, it promoted cell death induced by pro-oxidants, which was attenuated in MSRA-deficient cells. When mice were exposed to hyperoxic conditions for 2 days, their livers and kidneys were injured and protein carbonylation was increased. The oxidative tissue injury was more severe in ARD1 transgenic mice than in their wild-type littermates. In conclusion, ARD1 has a crucial role in the cellular response to oxidative stress as a bona fide regulator of MSRA. ARD1 is a potential target for ameliorating oxidative injury or for potentiating ROS-producing anticancer agents.
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114
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Tooley JG, Schaner Tooley CE. New roles for old modifications: emerging roles of N-terminal post-translational modifications in development and disease. Protein Sci 2014; 23:1641-9. [PMID: 25209108 DOI: 10.1002/pro.2547] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/08/2014] [Indexed: 01/07/2023]
Abstract
The importance of internal post-translational modification (PTM) in protein signaling and function has long been known and appreciated. However, the significance of the same PTMs on the alpha amino group of N-terminal amino acids has been comparatively understudied. Historically considered static regulators of protein stability, additional functional roles for N-terminal PTMs are now beginning to be elucidated. New findings show that N-terminal methylation, along with N-terminal acetylation, is an important regulatory modification with significant roles in development and disease progression. There are also emerging studies on the enzymology and functional roles of N-terminal ubiquitylation and N-terminal propionylation. Here, will discuss the recent advances in the functional studies of N-terminal PTMs, recount the new N-terminal PTMs being identified, and briefly examine the possibility of dynamic N-terminal PTM exchange.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry and Molecular Biology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky
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115
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Lee KE, Ahn JY, Kim JM, Hwang CS. Synthetic lethal screen of NAA20, a catalytic subunit gene of NatB N-terminal acetylase in Saccharomyces cerevisiae. J Microbiol 2014; 52:842-8. [PMID: 25163837 DOI: 10.1007/s12275-014-3694-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023]
Abstract
The Saccharomyces cerevisiae NatB N-terminal acetylase contains a catalytic subunit Naa20 and an auxiliary subunit Naa25. To elucidate the cellular functions of the NatB, we utilized the Synthetic Genetic Array to screen for genes that are essential for cell growth in the absence of NAA20. The genome-wide synthetic lethal screen of NAA20 identified genes encoding for serine/threonine protein kinase Vps15, 1,3-beta-glucanosyltransferase Gas5, and a catabolic repression regulator Mig3. The present study suggests that the catalytic activity of the NatB N-terminal aceytase is involved in vacuolar protein sorting and cell wall maintenance.
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Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Gyeongbuk, 790-784, Republic of Korea
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116
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Ma C, Pathak C, Jang S, Lee SJ, Nam M, Kim SJ, Im H, Lee BJ. Structure of Thermoplasma volcanium Ard1 belongs to N-acetyltransferase family member suggesting multiple ligand binding modes with acetyl coenzyme A and coenzyme A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1790-7. [PMID: 25062911 DOI: 10.1016/j.bbapap.2014.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
Abstract
Acetylation and deacetylation reactions result in biologically important modifications that are involved in normal cell function and cancer development. These reactions, carried out by protein acetyltransferase enzymes, act by transferring an acetyl group from acetyl-coenzymeA (Ac-CoA) to various substrate proteins. Such protein acetylation remains poorly understood in Archaea, and has been only partially described. Information processing in Archaea has been reported to be similar to that in eukaryotes and distinct from the equivalent bacterial processes. The human N-acetyltransferase Ard1 (hArd1) is one of the acetyltransferases that has been found to be overexpressed in various cancer cells and tissues, and knockout of the hArd1 gene significantly reduces growth rate of the cancer cell lines. In the present study, we determined the crystal structure of Thermoplasma volcanium Ard1 (Tv Ard1), which shows both ligand-free and multiple ligand-bound forms, i.e.,Ac-CoA- and coenzyme A (CoA)-bound forms. The difference between ligand-free and ligand-bound chains in the crystal structure was used to search for the interacting residues. The re-orientation and position of the loop between β4 and α3 including the phosphate-binding loop (P-loop) were observed, which are important for the ligand interaction. In addition, a biochemical assay to determine the N-acetyltransferase activity of Tv Ard1 was performed using the T.volcanium substrate protein Alba (Tv Alba). Taken together, the findings of this study elucidate ligand-free form of Tv Ard1 for the first time and suggest multiple modes of binding with Ac-CoA and CoA.
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Affiliation(s)
- Chao Ma
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Chinar Pathak
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Sunbok Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Sang Jae Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Minjoo Nam
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea.
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117
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Holmes WM, Mannakee BK, Gutenkunst RN, Serio TR. Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding. Nat Commun 2014; 5:4383. [PMID: 25023910 PMCID: PMC4140192 DOI: 10.1038/ncomms5383] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
N-terminal acetylation is among the most ubiquitous of protein modifications in eukaryotes. While loss of N-terminal acetylation is associated with many abnormalities, the molecular basis of these effects is known for only a few cases, where acetylation of single factors has been linked to binding avidity or metabolic stability. In contrast, the impact of N-terminal acetylation for the majority of the proteome, and its combinatorial contributions to phenotypes, are unknown. Here, by studying the yeast prion [PSI+], an amyloid of the Sup35 protein, we show that loss of N-terminal acetylation promotes general protein misfolding, a redeployment of chaperones to these substrates, and a corresponding stress response. These proteostasis changes, combined with the decreased stability of unacetylated Sup35 amyloid, reduce the size of prion aggregates and reverse their phenotypic consequences. Thus, loss of N-terminal acetylation, and its previously unanticipated role in protein biogenesis, globally resculpts the proteome to create a unique phenotype.
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Affiliation(s)
- William M Holmes
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
| | - Brian K Mannakee
- Graduate Interdisciplinary Program in Statistics, University of Arizona, 1548 East Drachman Street, Tucson, Arizona 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona 85721, USA
| | - Tricia R Serio
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
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118
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Zeng Y, Min L, Han Y, Meng L, Liu C, Xie Y, Dong B, Wang L, Jiang B, Xu H, Zhuang Q, Zhao C, Qu L, Shou C. Inhibition of STAT5a by Naa10p contributes to decreased breast cancer metastasis. Carcinogenesis 2014; 35:2244-53. [DOI: 10.1093/carcin/bgu132] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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119
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Van Damme P, Støve SI, Glomnes N, Gevaert K, Arnesen T. A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant. Mol Cell Proteomics 2014; 13:2031-41. [PMID: 24408909 DOI: 10.1074/mcp.m113.035402] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) occurs on the majority of eukaryotic proteins and is catalyzed by N-terminal acetyltransferases (NATs). Nt-acetylation is increasingly recognized as a vital modification with functional implications ranging from protein degradation to protein localization. Although early genetic studies in yeast demonstrated that NAT-deletion strains displayed a variety of phenotypes, only recently, the first human genetic disorder caused by a mutation in a NAT gene was reported; boys diagnosed with the X-linked Ogden syndrome harbor a p.Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of the NatA complex, and suffer from global developmental delays and lethality during infancy. Here, we describe a Saccharomyces cerevisiae model developed by introducing the human wild-type or mutant NatA complex into yeast lacking NatA (NatA-Δ). The wild-type human NatA complex phenotypically complemented the NatA-Δ strain, whereas only a partial rescue was observed for the Ogden mutant NatA complex suggesting that hNaa10 S37P is only partially functional in vivo. Immunoprecipitation experiments revealed a reduced subunit complexation for the mutant hNatA S37P next to a reduced in vitro catalytic activity. We performed quantitative Nt-acetylome analyses on a control yeast strain (yNatA), a yeast NatA deletion strain (yNatA-Δ), a yeast NatA deletion strain expressing wild-type human NatA (hNatA), and a yeast NatA deletion strain expressing mutant human NatA (hNatA S37P). Interestingly, a generally reduced degree of Nt-acetylation was observed among a large group of NatA substrates in the yeast expressing mutant hNatA as compared with yeast expressing wild-type hNatA. Combined, these data provide strong support for the functional impairment of hNaa10 S37P in vivo and suggest that reduced Nt-acetylation of one or more target substrates contributes to the pathogenesis of the Ogden syndrome. Comparative analysis between human and yeast NatA also provided new insights into the co-evolution of the NatA complexes and their substrates. For instance, (Met-)Ala- N termini are more prevalent in the human proteome as compared with the yeast proteome, and hNatA displays a preference toward these N termini as compared with yNatA.
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Affiliation(s)
- Petra Van Damme
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium;
| | - Svein I Støve
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Nina Glomnes
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; ‖Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; and
| | - Kris Gevaert
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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120
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Liszczak G, Goldberg JM, Foyn H, Petersson EJ, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by the heterodimeric NatA complex. Nat Struct Mol Biol 2013; 20:1098-105. [PMID: 23912279 PMCID: PMC3766382 DOI: 10.1038/nsmb.2636] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/19/2013] [Indexed: 12/23/2022]
Abstract
Amino-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this co-translational modification, the heterodimeric NatA complex harbors the most diversity for substrate selection and modifies the majority of all amino-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100 kDa holo-NatA complex from Schizosaccharomyces pombe in the absence and presence of a bisubstrate peptide-CoA conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 TPR motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.
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Affiliation(s)
- Glen Liszczak
- 1] Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania, USA. [2] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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121
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N-α-acetyltransferase 10 protein is a negative regulator of 28S proteasome through interaction with PA28β. FEBS Lett 2013; 587:1630-7. [PMID: 23624078 DOI: 10.1016/j.febslet.2013.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/10/2013] [Accepted: 04/02/2013] [Indexed: 01/10/2023]
Abstract
N-α-acetyltransferase 10 protein (Naa10p) regulates various pathways associated with cancer cell proliferation, metastasis, apoptosis and autophagy. However, its role in protein quality control is unknown. Here, we report that Naa10p is physically associated with proteasome activator 28β (PA28β). Naa10p also interacts with PA28α in a PA28β-dependent manner. Naa10p negatively regulates PA28-dependent chymotrypsin-like proteasome activity in cancer cells and in a cell-free system reconstituted with purified proteins, which is not related to 26S proteasome. Acetyltransferase activity of Naa10p is not required for its effect on chymotrypsin-like proteasome activity. Therefore, our data reveal that Naa10p suppresses 28S proteasome activity through interaction with PA28β.
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122
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Foyn H, Jones JE, Lewallen D, Narawane R, Varhaug JE, Thompson PR, Arnesen T. Design, synthesis, and kinetic characterization of protein N-terminal acetyltransferase inhibitors. ACS Chem Biol 2013; 8:1121-7. [PMID: 23557624 DOI: 10.1021/cb400136s] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The N-termini of 80-90% of human proteins are acetylated by the N-terminal acetyltransferases (NATs), NatA-NatF. The major NAT complex, NatA, and particularly the catalytic subunit hNaa10 (ARD1) has been implicated in cancer development. For example, knockdown of hNaa10 results in cancer cell death and the arrest of cell proliferation. It also sensitized cancer cells to drug-induced cytotoxicity. Human NatE has a distinct substrate specificity and is essential for normal chromosome segregation. Thus, NAT inhibitors may potentially be valuable anticancer therapeutics, either directly or as adjuvants. Herein, we report the design and synthesis of the first inhibitors targeting these enzymes. Using the substrate specificity of the enzymes as a guide, we synthesized three bisubstrate analogues that potently and selectively inhibit the NatA complex (CoA-Ac-SES4; IC50 = 15.1 μM), hNaa10, the catalytic subunit of NatA (CoA-Ac-EEE4; Ki = 1.6 μM), and NatE/hNaa50 (CoA-Ac-MLG7; Ki* = 8 nM); CoA-Ac-EEE4 is a reversible competitive inhibitor of hNaa10, and CoA-Ac-MLG7 is a slow tight binding inhibitor of hNaa50. Our demonstration that it is possible to develop NAT selective inhibitors should assist future efforts to develop NAT inhibitors with more drug-like properties that can be used to chemically interrogate in vivo NAT function.
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Affiliation(s)
- Håvard Foyn
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
- Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Justin E. Jones
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Dan Lewallen
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Rashmi Narawane
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Jan Erik Varhaug
- Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
- Department of Surgical Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Paul R. Thompson
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
- Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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123
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Monda JK, Scott DC, Miller DJ, Lydeard J, King D, Harper JW, Bennett EJ, Schulman BA. Structural conservation of distinctive N-terminal acetylation-dependent interactions across a family of mammalian NEDD8 ligation enzymes. Structure 2013; 21:42-53. [PMID: 23201271 PMCID: PMC3786212 DOI: 10.1016/j.str.2012.10.013] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/20/2012] [Accepted: 10/25/2012] [Indexed: 01/07/2023]
Abstract
Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like protein NEDD8 to cullin targets, recognizes acetylated N termini of the E2 enzymes UBC12 and UBE2F. Systematic biochemical and biophysical analyses reveal 40- and 10-fold variations in affinities among different DCNL-cullin and DCNL-E2 complexes, contributing to varying efficiencies of different NEDD8 ligation cascades. Structures of DCNL2 and DCNL3 complexes with N-terminally acetylated peptides from UBC12 and UBE2F illuminate a common mechanism by which DCNL proteins recognize N-terminally acetylated E2s and how selectivity for interactions dependent on N-acetyl-methionine are established through side chains recognizing distal residues. Distinct preferences of UBC12 and UBE2F peptides for inhibiting different DCNLs, including the oncogenic DCNL1 protein, suggest it may be possible to develop small molecules blocking specific N-acetyl-methionine-dependent protein interactions.
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Affiliation(s)
- Julie K. Monda
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - Daniel C. Scott
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105,Department of Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - Darcie J. Miller
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - John Lydeard
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - David King
- HHMI Mass Spectrometry Laboratory, University of California, Berkeley CA 94720
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - Eric J. Bennett
- Department of Cell Biology, Harvard Medical School, Boston MA 02115,Division of Biological Sciences, University of California San Diego, La Jolla CA 92093
| | - Brenda A. Schulman
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105,Department of Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis TN, 38105
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