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Heathcote KC, Keeley TP, Myllykoski M, Lundekvam M, McTiernan N, Akter S, Masson N, Ratcliffe PJ, Arnesen T, Flashman E. N-terminal cysteine acetylation and oxidation patterns may define protein stability. Nat Commun 2024; 15:5360. [PMID: 38918375 PMCID: PMC11199558 DOI: 10.1038/s41467-024-49489-2] [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: 08/17/2023] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Oxygen homeostasis is maintained in plants and animals by O2-sensing enzymes initiating adaptive responses to low O2 (hypoxia). Recently, the O2-sensitive enzyme ADO was shown to initiate degradation of target proteins RGS4/5 and IL32 via the Cysteine/Arginine N-degron pathway. ADO functions by catalysing oxidation of N-terminal cysteine residues, but despite multiple proteins in the human proteome having an N-terminal cysteine, other endogenous ADO substrates have not yet been identified. This could be because alternative modifications of N-terminal cysteine residues, including acetylation, prevent ADO-catalysed oxidation. Here we investigate the relationship between ADO-catalysed oxidation and NatA-catalysed acetylation of a broad range of protein sequences with N-terminal cysteines. We present evidence that human NatA catalyses N-terminal cysteine acetylation in vitro and in vivo. We then show that sequences downstream of the N-terminal cysteine dictate whether this residue is oxidised or acetylated, with ADO preferring basic and aromatic amino acids and NatA preferring acidic or polar residues. In vitro, the two modifications appear to be mutually exclusive, suggesting that distinct pools of N-terminal cysteine proteins may be acetylated or oxidised. These results reveal the sequence determinants that contribute to N-terminal cysteine protein modifications, with implications for O2-dependent protein stability and the hypoxic response.
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Affiliation(s)
- Karen C Heathcote
- Department of Chemistry, University of Oxford, OX1 3TA, Oxford, UK
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Thomas P Keeley
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Matti Myllykoski
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Malin Lundekvam
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Salma Akter
- Department of Chemistry, University of Oxford, OX1 3TA, Oxford, UK
| | - Norma Masson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK.
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, 5021, Bergen, Norway.
| | - Emily Flashman
- Department of Biology, University of Oxford, OX1 3RB, Oxford, UK.
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2
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Alsaker NE, Halskau Ø, Haug BE, Reuter N, Nerdal W. Phospholipid Membrane Interactions of Model Ac-WL-X-LL-OH Peptides Investigated by Solid-State Nuclear Magnetic Resonance. MEMBRANES 2024; 14:105. [PMID: 38786939 PMCID: PMC11123086 DOI: 10.3390/membranes14050105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The role of aromatic amino acids in peripheral protein membrane binding has been reported to involve cation-π interactions with choline lipids. In this study, we have investigated the interactions of the model pentapeptide Ac-WL-X-LL-OH (where X = L, Y, F, or W) with the phospholipid membrane using solid-state NMR. The effect of guest residue X on the peptide-lipid interactome was complementary to the seminal report on the interfacial hydrophobicity scale by Wimley and White. We found that the phospholipids retained a lamellar phase in the presence of each of the peptides with an aromatic X residue, whereas the Leu peptide perturbed the bilayer to an extent where an additional isotropic phase was observed. The solid-state NMR 13C and 31P data provide additional information on the influence of these short peptides on the membrane that has not been previously reported. The magnitude of membrane perturbation was in the order of guest residue X = L > Y~F > W, which is consistent with the relative amino acid interfacial affinity reported by Wimley and White. Further work is, however, required to uncover the behavior of the peptide and localization in the membrane domain due to ambiguity of the 13C NMR data. We have launched efforts in this regard for the objective of better understanding the role of aromatic amino acids in peripheral membrane protein binding.
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Affiliation(s)
- Nicolai Etwin Alsaker
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53A, N-5006 Bergen, Norway;
| | - Bengt Erik Haug
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Willy Nerdal
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway; (B.E.H.); (N.R.); (W.N.)
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3
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Chelban V, Aksnes H, Maroofian R, LaMonica LC, Seabra L, Siggervåg A, Devic P, Shamseldin HE, Vandrovcova J, Murphy D, Richard AC, Quenez O, Bonnevalle A, Zanetti MN, Kaiyrzhanov R, Salpietro V, Efthymiou S, Schottlaender LV, Morsy H, Scardamaglia A, Tariq A, Pagnamenta AT, Pennavaria A, Krogstad LS, Bekkelund ÅK, Caiella A, Glomnes N, Brønstad KM, Tury S, Moreno De Luca A, Boland-Auge A, Olaso R, Deleuze JF, Anheim M, Cretin B, Vona B, Alajlan F, Abdulwahab F, Battini JL, İpek R, Bauer P, Zifarelli G, Gungor S, Kurul SH, Lochmuller H, Da'as SI, Fakhro KA, Gómez-Pascual A, Botía JA, Wood NW, Horvath R, Ernst AM, Rothman JE, McEntagart M, Crow YJ, Alkuraya FS, Nicolas G, Arnesen T, Houlden H. Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications. Nat Commun 2024; 15:2269. [PMID: 38480682 PMCID: PMC10937998 DOI: 10.1038/s41467-024-46354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Primary familial brain calcification (PFBC) is characterized by calcium deposition in the brain, causing progressive movement disorders, psychiatric symptoms, and cognitive decline. PFBC is a heterogeneous disorder currently linked to variants in six different genes, but most patients remain genetically undiagnosed. Here, we identify biallelic NAA60 variants in ten individuals from seven families with autosomal recessive PFBC. The NAA60 variants lead to loss-of-function with lack of protein N-terminal (Nt)-acetylation activity. We show that the phosphate importer SLC20A2 is a substrate of NAA60 in vitro. In cells, loss of NAA60 caused reduced surface levels of SLC20A2 and a reduction in extracellular phosphate uptake. This study establishes NAA60 as a causal gene for PFBC, provides a possible biochemical explanation of its disease-causing mechanisms and underscores NAA60-mediated Nt-acetylation of transmembrane proteins as a fundamental process for healthy neurobiological functioning.
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Affiliation(s)
- Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
- Neurobiology and Medical Genetics Laboratory, "Nicolae Testemitanu" State University of Medicine and Pharmacy, 165, Stefan cel Mare si Sfant Boulevard, MD, 2004, Chisinau, Republic of Moldova.
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Lauren C LaMonica
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Luis Seabra
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France
| | | | - Perrine Devic
- Hospices Civils de Lyon, Groupement Hospitalier Sud, Service d'Explorations Fonctionnelles Neurologiques, Lyon, France
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Anne-Claire Richard
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Antoine Bonnevalle
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - M Natalia Zanetti
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- South Kazakhstan Medical Academy Shymkent, Shymkent, 160019, Kazakhstan
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Lucia V Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Av. Juan Domingo Perón 1500, B1629AHJ, Pilar, Argentina
- Instituto de medicina genómica (IMeG), Hospital Universitario Austral, Universidad Austral, Av. Juan Domingo Perón 1500, B1629AHJ, Pilar, Argentina
| | - Heba Morsy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Annarita Scardamaglia
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Ambreen Tariq
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Ajia Pennavaria
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Liv S Krogstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Åse K Bekkelund
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Alessia Caiella
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5020, Bergen, Norway
| | | | - Sandrine Tury
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Andrés Moreno De Luca
- Department of Radiology, Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Mathieu Anheim
- Neurology Department, Strasbourg University Hospital, Strasbourg, France
- Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg, France
- INSERM-U964; CNRS-UMR7104, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Benjamin Cretin
- Neurology Department, Strasbourg University Hospital, Strasbourg, France
- Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg, France
- INSERM-U964; CNRS-UMR7104, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Fahad Alajlan
- Department of Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jean-Luc Battini
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Rojan İpek
- Paediatric Neurology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Peter Bauer
- Centogene GmbH, Am Strande 7, 18055, Rostock, Germany
| | | | - Serdal Gungor
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Pediatrics, Division of Pediatric Neurology, Malatya, Turkey
| | - Semra Hiz Kurul
- Dokuz Eylul University, School of Medicine, Department of Paediatric Neurology, Izmir, Turkey
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute and Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Sahar I Da'as
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Weill Cornell Medical College, Doha, Qatar
| | - Alicia Gómez-Pascual
- Department of Information and Communications Engineering, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
| | - Juan A Botía
- Department of Information and Communications Engineering, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Andreas M Ernst
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - James E Rothman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Meriel McEntagart
- Medical Genetics Department, St George's University Hospitals, London, SWI7 0RE, UK
| | - Yanick J Crow
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
- Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK.
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4
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Etherington RD, Bailey M, Boyer JB, Armbruster L, Cao X, Coates JC, Meinnel T, Wirtz M, Giglione C, Gibbs DJ. Nt-acetylation-independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases. PLANT PHYSIOLOGY 2023; 193:2086-2104. [PMID: 37427787 PMCID: PMC10602611 DOI: 10.1093/plphys/kiad406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
The acetylation-dependent (Ac/)N-degron pathway degrades proteins through recognition of their acetylated N-termini (Nt) by E3 ligases called Ac/N-recognins. To date, specific Ac/N-recognins have not been defined in plants. Here we used molecular, genetic, and multiomics approaches to characterize potential roles for Arabidopsis (Arabidopsis thaliana) DEGRADATION OF ALPHA2 10 (DOA10)-like E3 ligases in the Nt-acetylation-(NTA)-dependent turnover of proteins at global- and protein-specific scales. Arabidopsis has two endoplasmic reticulum (ER)-localized DOA10-like proteins. AtDOA10A, but not the Brassicaceae-specific AtDOA10B, can compensate for loss of yeast (Saccharomyces cerevisiae) ScDOA10 function. Transcriptome and Nt-acetylome profiling of an Atdoa10a/b RNAi mutant revealed no obvious differences in the global NTA profile compared to wild type, suggesting that AtDOA10s do not regulate the bulk turnover of NTA substrates. Using protein steady-state and cycloheximide-chase degradation assays in yeast and Arabidopsis, we showed that turnover of ER-localized SQUALENE EPOXIDASE 1 (AtSQE1), a critical sterol biosynthesis enzyme, is mediated by AtDOA10s. Degradation of AtSQE1 in planta did not depend on NTA, but Nt-acetyltransferases indirectly impacted its turnover in yeast, indicating kingdom-specific differences in NTA and cellular proteostasis. Our work suggests that, in contrast to yeast and mammals, targeting of Nt-acetylated proteins is not a major function of DOA10-like E3 ligases in Arabidopsis and provides further insight into plant ERAD and the conservation of regulatory mechanisms controlling sterol biosynthesis in eukaryotes.
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Affiliation(s)
- Ross D Etherington
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Mark Bailey
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Jean-Baptiste Boyer
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Laura Armbruster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Xulyu Cao
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Thierry Meinnel
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Carmela Giglione
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
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5
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Abstract
Most proteins receive an acetyl group at the N terminus while in their nascency as the result of modification by co-translationally acting N-terminal acetyltransferases (NATs). The N-terminal acetyl group can influence several aspects of protein functionality. From studies of NAT-lacking cells, it is evident that several cellular processes are affected by this modification. More recently, an increasing number of genetic cases have demonstrated that N-terminal acetylation has crucial roles in human physiology and pathology. In this Cell Science at a Glance and the accompanying poster, we provide an overview of the human NAT enzymes and their properties, substrate coverage, cellular roles and connections to human disease.
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Affiliation(s)
- Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Department of Biological Sciences, University of Bergen, 5009 Bergen, Norway
- Department of Surgery, Haukeland University Hospital, 5009 Bergen, Norway
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6
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Pan B, Gardner SM, Schultz K, Perez RM, Deng S, Shimogawa M, Sato K, Rhoades E, Marmorstein R, Petersson EJ. Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies. J Am Chem Soc 2023; 145:14019-14030. [PMID: 37319422 PMCID: PMC10728591 DOI: 10.1021/jacs.3c03887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases. A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here, we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes as well as their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Sarah M. Gardner
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kollin Schultz
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryann M. Perez
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Sunbin Deng
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marie Shimogawa
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Kohei Sato
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Elizabeth Rhoades
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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7
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Pan B, Gardner S, Schultz K, Perez RM, Deng S, Shimogawa M, Sato K, Rhoades E, Marmorstein R, Petersson EJ. Semi-synthetic CoA-α-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535351. [PMID: 37066334 PMCID: PMC10104007 DOI: 10.1101/2023.04.03.535351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes and their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
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8
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Donnarumma F, Tucci V, Ambrosino C, Altucci L, Carafa V. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. Clin Epigenetics 2022; 14:182. [PMID: 36539894 PMCID: PMC9769039 DOI: 10.1186/s13148-022-01402-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Chromatin structural organization, gene expression and proteostasis are intricately regulated in a wide range of biological processes, both physiological and pathological. Protein acetylation, a major post-translational modification, is tightly involved in interconnected biological networks, modulating the activation of gene transcription and protein action in cells. A very large number of studies describe the pivotal role of the so-called acetylome (accounting for more than 80% of the human proteome) in orchestrating different pathways in response to stimuli and triggering severe diseases, including cancer. NAA60/NatF (N-terminal acetyltransferase F), also named HAT4 (histone acetyltransferase type B protein 4), is a newly discovered acetyltransferase in humans modifying N-termini of transmembrane proteins starting with M-K/M-A/M-V/M-M residues and is also thought to modify lysine residues of histone H4. Because of its enzymatic features and unusual cell localization on the Golgi membrane, NAA60 is an intriguing acetyltransferase that warrants biochemical and clinical investigation. Although it is still poorly studied, this review summarizes current findings concerning the structural hallmarks and biological role of this novel targetable epigenetic enzyme.
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Affiliation(s)
- Federica Donnarumma
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy
| | - Valeria Tucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Concetta Ambrosino
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.47422.370000 0001 0724 3038Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Lucia Altucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Vincenzo Carafa
- grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
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9
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Pożoga M, Armbruster L, Wirtz M. From Nucleus to Membrane: A Subcellular Map of the N-Acetylation Machinery in Plants. Int J Mol Sci 2022; 23:ijms232214492. [PMID: 36430970 PMCID: PMC9692967 DOI: 10.3390/ijms232214492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
N-terminal acetylation (NTA) is an ancient protein modification conserved throughout all domains of life. N-terminally acetylated proteins are present in the cytosol, the nucleus, the plastids, mitochondria and the plasma membrane of plants. The frequency of NTA differs greatly between these subcellular compartments. While up to 80% of cytosolic and 20-30% of plastidic proteins are subject to NTA, NTA of mitochondrial proteins is rare. NTA alters key characteristics of proteins such as their three-dimensional structure, binding properties and lifetime. Since the majority of proteins is acetylated by five ribosome-bound N-terminal acetyltransferases (Nats) in yeast and humans, NTA was long perceived as an exclusively co-translational process in eukaryotes. The recent characterization of post-translationally acting plant Nats, which localize to the plasma membrane and the plastids, has challenged this view. Moreover, findings in humans, yeast, green algae and higher plants uncover differences in the cytosolic Nat machinery of photosynthetic and non-photosynthetic eukaryotes. These distinctive features of the plant Nat machinery might constitute adaptations to the sessile lifestyle of plants. This review sheds light on the unique role of plant N-acetyltransferases in development and stress responses as well as their evolution-driven adaptation to function in different cellular compartments.
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10
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Weidenhausen J, Kopp J, Ruger-Herreros C, Stein F, Haberkant P, Lapouge K, Sinning I. Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity. Int J Mol Sci 2022; 23:ijms231810805. [PMID: 36142717 PMCID: PMC9500918 DOI: 10.3390/ijms231810805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most eukaryotic proteins are N-terminally acetylated by a set of Nα acetyltransferases (NATs). This ancient and ubiquitous modification plays a fundamental role in protein homeostasis, while mutations are linked to human diseases and phenotypic defects. In particular, Naa50 features species-specific differences, as it is inactive in yeast but active in higher eukaryotes. Together with NatA, it engages in NatE complex formation for cotranslational acetylation. Here, we report Naa50 homologs from the filamentous fungi Chaetomium thermophilum and Neurospora crassa with significant N- and C-terminal extensions to the conserved GNAT domain. Structural and biochemical analyses show that CtNaa50 shares the GNAT structure and substrate specificity with other homologs. However, in contrast to previously analyzed Naa50 proteins, it does not form NatE. The elongated N-terminus increases Naa50 thermostability and binds to dynein light chain protein 1, while our data suggest that conserved positive patches in the C-terminus allow for ribosome binding independent of NatA. Our study provides new insights into the many facets of Naa50 and highlights the diversification of NATs during evolution.
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Affiliation(s)
- Jonas Weidenhausen
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Carmen Ruger-Herreros
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Center for Molecular Biology of the University of Heidelberg (ZMBH), 69120 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Correspondence:
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11
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Brahma R, Raghuraman H. Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins. J Membr Biol 2022; 255:469-483. [PMID: 35274157 DOI: 10.1007/s00232-022-00224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
The structural organization and dynamic nature of the biomembrane components are important determinants for numerous cellular functions. Particularly, membrane proteins are critically important for various physiological functions and are important drug targets. The mechanistic insights on the complex functionality of membrane lipids and proteins can be elucidated by understanding the interplay between structure and dynamics. In this regard, membrane penetration depth represents an important parameter to obtain the precise depth of membrane-embedded molecules that often define the conformation and topology of membrane probes and proteins. In this review, we discuss about the widely used fluorescence quenching-based methods (parallax method, distribution analysis, and dual-quencher analysis) to accurately determine the membrane penetration depths of fluorescent probes that are either membrane-embedded or attached to lipids and proteins. Further, we also discuss a relatively novel fluorescence quenching method that utilizes tryptophan residue as the quencher, namely the tryptophan-induced quenching, which is sensitive to monitor small-scale conformational changes (short distances of < 15 Å) and useful in mapping distances in proteins. We have provided numerous examples for the benefit of readers to appreciate the importance and applicability of these simple yet powerful methods to study membrane proteins.
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Affiliation(s)
- Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF, Bidhannagar, Kolkata, 700 064, India.
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12
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Moutoussamy EE, Waheed Q, Binford GJ, Khan HM, Moran SM, Eitel AR, Cordes MHJ, Reuter N. Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage. PLoS Comput Biol 2022; 18:e1009871. [PMID: 35180220 PMCID: PMC8893692 DOI: 10.1371/journal.pcbi.1009871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/03/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments. Envenomation following bites from recluse spiders (Loxosceles) causes loxoscelism, a necrotic tissue breakdown in mammals, and leads to skin degeneration and systemic reactions in the worst case. Recluse spiders belong to the Sicariidae family which also includes six-eyed sand spiders in the genera Sicarius and Hexopthalma. While sicariid spiders are found natively on all continents except Australia, treatments of loxoscelism are typically antibody based and available in some regions of the Americas. Sphingomyelinase D/phospholipase D enzymes are one of the major toxins in venom of sicariid spiders, and have been divided in two clades called α and β. The activity of α and β clades toxins differs; most α clade toxins present high activity against lipids with choline headgroups (-N (CH3)3+) such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (-NH3+). When comparing the structures of two α clade toxins and one β clade toxin, we noticed the presence in the α clade toxins only of a cage consisting of three aromatic amino acids. In this work we used numerical molecular simulations to probe the role of this cage in the preference of α clade toxins for choline head groups over ethanolamine head groups.
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Affiliation(s)
- Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Qaiser Waheed
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Greta J. Binford
- Department of Biology, Lewis and Clark College, Portland, Oregon, United States
| | - Hanif M. Khan
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Shane M. Moran
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Matthew H. J. Cordes
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
- * E-mail:
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13
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Mok JW, Choi KW. Modulation of Hippo signaling by Mnat9 N-acetyltransferase for normal growth and tumorigenesis in Drosophila. Cell Death Dis 2022; 13:101. [PMID: 35110540 PMCID: PMC8810759 DOI: 10.1038/s41419-022-04532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 12/25/2021] [Accepted: 01/13/2022] [Indexed: 11/09/2022]
Abstract
AbstractHippo signaling is a conserved mechanism for controlling organ growth. Increasing evidence suggests that Hippo signaling is modulated by various cellular factors for normal development and tumorigenesis. Hence, identification of these factors is pivotal for understanding the mechanism for the regulation of Hippo signaling. Drosophila Mnat9 is a putative N-acetyltransferase that is required for cell survival by affecting JNK signaling. Here we show that Mnat9 is involved in the negative regulation of Hippo signaling. RNAi knockdown of Mnat9 in the eye disc suppresses the rough eye phenotype of overexpressing Crumbs (Crb), an upstream factor of the Hippo pathway. Conversely, Mnat9 RNAi enhances the eye phenotype caused by overexpressing Expanded (Ex) or Warts (Wts) that acts downstream to Crb. Similar genetic interactions between Mnat9 and Hippo pathway genes are found in the wing. The reduced wing phenotype of Mnat9 RNAi is suppressed by overexpression of Yorkie (Yki), while it is suppressed by knockdown of Hippo upstream factors like Ex, Merlin, or Kibra. Mnat9 co-immunoprecipitates with Mer, implying their function in a protein complex. Furthermore, Mnat9 overexpression together with Hpo knockdown causes tumorous overgrowth in the abdomen. Our data suggest that Mnat9 is required for organ growth and can induce tumorous growth by negatively regulating the Hippo signaling pathway.
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14
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Ahmed F, Husain M. Human N-Alpha-Acetyltransferase 60 Promotes Influenza A Virus Infection by Dampening the Interferon Alpha Signaling. Front Immunol 2022; 12:771792. [PMID: 35095845 PMCID: PMC8790067 DOI: 10.3389/fimmu.2021.771792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
N-alpha-acetyltransferase 60 (NAA60) is the most recently discovered N-terminal acetyltransferase and found only in multicellular eukaryotes. NAA60 localizes to the Golgi complex and is one of the only two N-terminal acetyltransferases known to localize to an organelle. Furthermore, NAA60 possesses a unique ability of catalyzing the acetylation of membrane-anchored proteins at the N-terminus and histones at the lysine side chains. Herein, we demonstrate that NAA60 exhibits proviral properties during influenza A virus (IAV) infection by interfering with the interferon (IFN) α signaling. We found that the depletion and overexpression of NAA60 reduced and enhanced, respectively, the IAV growth in a cell type- and IAV strain-independent manner. Mechanistically, the IAV-induced expression of IFNα was increased and decreased in NAA60-depleted and -overexpressing cells, respectively. Furthermore, the depletion of NAA60 enhanced the level of phosphorylated STAT1 transcription factor as well as the expression of several IFN-stimulated genes (ISGs) such as MX1, CH25H, IFITM3, ISG15 and viperin in infected cells. Whereas the overexpression of NAA60 produced opposite results. Finally, similar results were obtained when the NAA60-depleted cells were treated with purified IFNα. These findings, in conjunction with our recent findings where N-terminal acetylation of many host proteins increased in response to the IAV infection, indicate an important role of N-terminal acetylation during IAV replication.
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15
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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16
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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17
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Krtenic B, Drazic A, Arnesen T, Reuter N. Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PLoS Comput Biol 2020; 16:e1007988. [PMID: 33362253 PMCID: PMC7790372 DOI: 10.1371/journal.pcbi.1007988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 01/07/2021] [Accepted: 10/16/2020] [Indexed: 11/19/2022] Open
Abstract
The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases. Enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily transfer an acetyl group from one molecule to another. This reaction is called acetylation and is one of the most common reactions inside the cell. The GNAT superfamily counts more than 870 000 members through all kingdoms of life. Despite sharing the same fold the GNAT superfamily is very diverse in terms of amino acid sequence and substrates. The eight N-terminal acetyltransferases (NatA, NatB, etc.. to NatH) are a GNAT subtype which acetylates the free amine group of polypeptide chains. This modification is called N-terminal acetylation and is one of the most abundant protein modifications in eukaryotic cells. This subtype is also characterized by a high sequence diversity even though they share the same substrate. In addition, the phylogeny of the superfamily is not characterized. This hampers functional annotation based on sequence similarity, and discovery of novel NATs. In this work we set out to solve the problem of the classification of eukaryotic GCN5-related acetyltransferases and report the first classification framework of the superfamily. This framework can be used as a tool for annotation of all GCN5-related acetyltransferases. As an example of what can be achieved we report in this paper the computational prediction and in vitro verification of the function of two previously uncharacterized N-terminal acetyltransferases. We also report the first acetyltransferase phylogenetic tree of the GCN5 superfamily. It indicates that N-terminal acetyltransferases do not constitute one homogeneous protein family, but that the ability to bind and acetylate protein N-termini had evolved more than once on the same acetylation scaffold. We also show that even small changes in key positions can lead to altered enzyme specificity.
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Affiliation(s)
- Bojan Krtenic
- Department of Biological Sciences, University of Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- * E-mail: (BK); (NR)
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, Norway
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Norway
- Department of Biomedicine, University of Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- Department of Chemistry, University of Bergen, Norway
- * E-mail: (BK); (NR)
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18
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Linster E, Layer D, Bienvenut WV, Dinh TV, Weyer FA, Leemhuis W, Brünje A, Hoffrichter M, Miklankova P, Kopp J, Lapouge K, Sindlinger J, Schwarzer D, Meinnel T, Finkemeier I, Giglione C, Hell R, Sinning I, Wirtz M. The Arabidopsis N α -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response. THE NEW PHYTOLOGIST 2020; 228:554-569. [PMID: 32548857 DOI: 10.1111/nph.16747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In humans and plants, N-terminal acetylation plays a central role in protein homeostasis, affects 80% of proteins in the cytoplasm and is catalyzed by five ribosome-associated N-acetyltransferases (NatA-E). Humans also possess a Golgi-associated NatF (HsNAA60) that is essential for Golgi integrity. Remarkably, NAA60 is absent in fungi and has not been identified in plants. Here we identify and characterize the first plasma membrane-anchored post-translationally acting N-acetyltransferase AtNAA60 in the reference plant Arabidopsis thaliana by the combined application of reverse genetics, global proteomics, live-cell imaging, microscale thermophoresis, circular dichroism spectroscopy, nano-differential scanning fluorometry, intrinsic tryptophan fluorescence and X-ray crystallography. We demonstrate that AtNAA60, like HsNAA60, is membrane-localized in vivo by an α-helical membrane anchor at its C-terminus, but in contrast to HsNAA60, AtNAA60 localizes to the plasma membrane. The AtNAA60 crystal structure provides insights into substrate-binding, the broad substrate specificity and the catalytic mechanism probed by structure-based mutagenesis. Characterization of the NAA60 loss-of-function mutants (naa60-1 and naa60-2) uncovers a plasma membrane-localized substrate of AtNAA60 and the importance of NAA60 during high salt stress. Our findings provide evidence for the plant-specific evolution of a plasma membrane-anchored N-acetyltransferase that is vital for adaptation to stress.
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Dominik Layer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Trinh V Dinh
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Felix A Weyer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Wiebke Leemhuis
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Marion Hoffrichter
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Ruediger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
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19
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Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation. Trends Biochem Sci 2020; 46:15-27. [PMID: 32912665 DOI: 10.1016/j.tibs.2020.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022]
Abstract
N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.
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20
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Beigl TB, Hellesvik M, Saraste J, Arnesen T, Aksnes H. N-terminal acetylation of actin by NAA80 is essential for structural integrity of the Golgi apparatus. Exp Cell Res 2020; 390:111961. [PMID: 32209306 DOI: 10.1016/j.yexcr.2020.111961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 01/07/2023]
Abstract
N-alpha-acetyltransferase 80 (NAA80) was recently demonstrated to acetylate the N-terminus of actin, with NAA80 knockout cells showing actin cytoskeleton-related phenotypes, such as increased formation of membrane protrusions and accelerated migration. Here we report that NAA80 knockout cells additionally display fragmentation of the Golgi apparatus. We further employed rescue assays to demonstrate that this phenotype is connected to the ability of NAA80 to modify actin. Thus, re-expression of NAA80, which leads to re-establishment of actin's N-terminal acetyl group, rescued the Golgi fragmentation, whereas a catalytic dead NAA80 mutant could neither restore actin Nt-acetylation nor Golgi structure. The Golgi phenotype of NAA80 KO cells was shared by both migrating and non-migrating cells and live-cell imaging indicated increased Golgi dynamics in migrating NAA80 KO cells. Finally, we detected a drastic increase in the amount of F-actin in cells lacking NAA80, suggesting a causal relationship between this effect and the observed re-organization of Golgi structure. The findings further underscore the importance of actin Nt-acetylation and provide novel insight into its cellular roles, suggesting a mechanistic link between actin modification state and Golgi organization.
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Affiliation(s)
- Tobias B Beigl
- Department of Biomedicine, University of Bergen, Norway; Institute of Cell Biology and Immunology, University of Stuttgart, Germany
| | | | | | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Norway; Department of Biological Sciences, University of Bergen, Norway; Department of Surgery, Haukeland University Hospital, Norway
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21
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Abboud A, Bédoucha P, Byška J, Arnesen T, Reuter N. Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases. Comput Struct Biotechnol J 2020; 18:532-547. [PMID: 32206212 PMCID: PMC7078549 DOI: 10.1016/j.csbj.2020.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
N-terminal acetyltransferases (NATs) belong to the superfamily of acetyltransferases. They are enzymes catalysing the transfer of an acetyl group from acetyl coenzyme A to the N-terminus of polypeptide chains. N-terminal acetylation is one of the most common protein modifications. To date, not much is known on the molecular basis for the exclusive substrate specificity of NATs. All NATs share a common fold called GNAT. A characteristic of NATs is the β6β7 hairpin loop covering the active site and forming with the α1α2 loop a narrow tunnel surrounding the catalytic site in which cofactor and polypeptide meet and exchange an acetyl group. We investigated the dynamics-function relationships of all available structures of NATs covering the three domains of Life. Using an elastic network model and normal mode analysis, we found a common dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove formed by the β4 and β5 strands and splitting the fold in two dynamical subdomains. Loops α1α2, β3β4 and β6β7 all show clear displacements in the low frequency normal modes. We characterized the mobility of the loops and show that even limited conformational changes of the loops along the low-frequency modes are able to significantly change the size and shape of the ligand binding sites. Based on the fact that these movements are present in most low-frequency modes, and common to all NATs, we suggest that the α1α2 and β6β7 loops may regulate ligand uptake and the release of the acetylated polypeptide.
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Affiliation(s)
- Angèle Abboud
- Department of Informatics, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pierre Bédoucha
- Department of Informatics, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jan Byška
- Department of Informatics, University of Bergen, Bergen, Norway
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
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22
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Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun 2020; 11:818. [PMID: 32042062 PMCID: PMC7010799 DOI: 10.1038/s41467-020-14584-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/18/2020] [Indexed: 01/04/2023] Open
Abstract
The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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23
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ZNF597 is a maternally expressed imprinted gene in the Holstein breed. Theriogenology 2020; 143:133-138. [PMID: 31874365 DOI: 10.1016/j.theriogenology.2019.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/24/2019] [Accepted: 12/14/2019] [Indexed: 11/22/2022]
Abstract
Genomic imprinting is an epigenetic phenomenon that leads to the preferential expression of genes from either the paternal or maternal allele. Imprinted genes play important roles in mammalian growth and development and a central role in placental function. ZNF597 and NAA60 are two paternally imprinted genes in the human ZNF597-NAA60 imprinted locus, both of which show biallelic expression in the mouse, but their imprinting status in cattle is still unknown. In this study, we examined the allelic expression of ZNF597 and NAA60 in adult bovine placental and somatic tissues. By comparing the mRNA-based genotypes with the genomic DNA-based genotypes, we identified monoallelic expression of ZNF597 in the placenta and in seven other tissues, including the cerebrum, heart, liver, spleen, lung, kidney, and muscle. Nevertheless, analysis revealed biallelic expression of the NAA60 gene in these tissues. Moreover, we tested the imprinting status of ZNF597 and confirmed that the maternal allele is expressed in the bovine placenta. To determine the role of DNA methylation in regulating monoallelic/imprinted expression of bovine ZNF597, the methylation status of two CpG-enriched regions in the bovine ZNF597-NAA60 locus was analyzed using the bisulfite sequencing method. Differentially methylated regions were detected on ten CpG loci in the bovine ZNF597 promoter region. In summary, the bovine ZNF597 gene is a maternally expressed gene, and its expression is regulated by DNA methylation, whereas the NAA60 gene is not imprinted in cattle.
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24
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Shao J, Zhang Y, Fan G, Xin Y, Yao Y. Transcriptome analysis identified a novel 3-LncRNA regulatory network of transthyretin attenuating glucose induced hRECs dysfunction in diabetic retinopathy. BMC Med Genomics 2019; 12:134. [PMID: 31615521 PMCID: PMC6794807 DOI: 10.1186/s12920-019-0596-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Diabetic retinopathy (DR) is the leading cause of blindness in the working age population. Transthyretin (TTR) showed a significantly decreased concentration in DR patients and exerted a visual protective effect by repressing neovascularization. This work intended to identify long non coding RNAs (lncRNAs) and explore their potential mechanism underlying the protective role of TTR. Methods Transcriptome of human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose (HG) or high glucose with 4 μM TTR (HG + TTR) was conducted. Differentially expressed lncRNAs, mRNAs and TTR related lncRNAs and mRNA were acquired. Functional annotation and Gene Set Enrichment Analysis were applied to analyse TTR affected pathways and processes. Weighted gene co-expression network analysis (WGCNA) was implemented to obtain hub modules and genes. LncRNA-mRNA regulatory networks were constructed based on cis, trans and competing endogenous RNAs acting mode. QRT-PCR was conducted to validate the expression of lncRNAs in aqueous humor and serum samples from 30 DR patients and 10 normal controls. Results RNA-sequencing of hRECs treated with low glucose (LG), high glucose (HG) or high glucose with 4 μM TTR (HG + TTR) was conducted. 146,783 protein-coding transcripts, 12,403 known lncRNA transcripts and 1184 novel non-coding transcripts were characterized. A total of 11,407 differentially expressed mRNAs (DE-mRNAs), 679 differentially expressed lncRNAs (DE-lncRNAs) in HG group versus LG group, 6206 DE-mRNAs and 194 DE-lncRNAs in HG + TTR versus HG group were obtained, respectively. 853 TTR-mRNAs and 48 TTR-lncRNAs were acquired, and functionally involved in cell cycle, apoptosis, inflammation signalling pathway, response to oxidative stress, neovascularization and autophagy. The WGCNA analysis identified a hub module of 133 genes, with the core function of oxidative stress response, angiogenesis, MAPK pathway, cell proliferation and apoptosis. After qRT-PCR validation, a 3-lncRNA regulatory network was proposed. At last, lncRNAs MSTRG.15047.3 and AC008403.3 showed significantly relative higher expression levels in both aqueous humor and serum samples, compared with normal controls, and FRMD6-AS2 was significantly down-regulated. Conclusions TTR regulated mRNAs and biological processes including oxidative stress, inflammation signalling and autophagy. A 3-lncRNA regulatory network was characterized underlying TTR repressing neovascularization, and showed potential diagnostic performance in DR.
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Affiliation(s)
- Jun Shao
- Department of Ophthalmology, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yunbin Zhang
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Guangming Fan
- Key Laboratory of Industry Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yu Xin
- Key Laboratory of Industry Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Yong Yao
- Department of Ophthalmology, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu, China.
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25
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Deng S, Magin RS, Wei X, Pan B, Petersson EJ, Marmorstein R. Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex. Structure 2019; 27:1057-1070.e4. [PMID: 31155310 PMCID: PMC6610660 DOI: 10.1016/j.str.2019.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 01/07/2023]
Abstract
NatA co-translationally acetylates the N termini of over 40% of eukaryotic proteins and can associate with another catalytic subunit, Naa50, to form a ternary NatA/Naa50 dual enzyme complex (also called NatE). The molecular basis of association between Naa50 and NatA and the mechanism for how their association affects their catalytic activities in yeast and human are poorly understood. Here, we determined the X-ray crystal structure of yeast NatA/Naa50 as a scaffold to understand coregulation of NatA/Naa50 activity in both yeast and human. We find that Naa50 makes evolutionarily conserved contacts to both the Naa10 and Naa15 subunits of NatA. These interactions promote catalytic crosstalk within the human complex, but do so to a lesser extent in the yeast complex, where Naa50 activity is compromised. These studies have implications for understanding the role of the NatA/Naa50 complex in modulating the majority of the N-terminal acetylome in diverse species.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert S Magin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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26
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Lyu C, Cai X. A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells. Virol J 2019; 16:81. [PMID: 31221185 PMCID: PMC6585060 DOI: 10.1186/s12985-019-1191-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudorabies virus (PRV) protein UL56 (pUL56) has been implicated in viral dissemination and virulence in vivo. However, the properties of PRV pUL56 remain largely unknown. In the present study, we aim to investigate the subcellular localization of pUL56 and the underlying molecular basis in transfected cells. METHODS Constructs of N-terminal green fluorescent protein (GFP) fused pUL56 and its truncations were employed for investigating subcellular localization and further identifying amino acids crucial for pUL56 localization in transfected Vero cells. Finally, the identified amino acids were replaced with alanine for confirming if these mutations could impair the specific localization of pUL56. RESULTS The pUL56 predominantly localized at the Golgi and trans-Golgi network (TGN) through its predicted C-terminal transmembrane helix in transfected Vero cells. A Golgi-associated protein Rab6a, independent of interaction with pUL56, was significantly downregulated by pUL56. Further, we found three truncated pUL56 C-terminal fragments (174-184, 175-185 and 191-195) could restrict GFP in the perinuclear region, respectively. Within these truncations, the 174proline (P), 181leucine (L), 185L and 191L were essential for maintaining perinuclear accumulation, thus suggesting an important role of leucine. Alanine (A) mutagenesis assays were employed to generate a series of pUL56 C-terminal mutants on the basis of leucine. Finally, a pUL56 mutant M10 (174P/A-177L/A-181L/A-185L/A-191L/A-194L/A-195I/A-196-197L/A-200L/A) lost Golgi-TGN localization. Thus, our data revealed that the leucine-rich transmembrane helix was responsible for pUL56 Golgi-TGN localization and retention, probably through specific intracellular membrane insertion. CONCLUSION Our data indicated that the C-terminal transmembrane helix was responsible for the Golgi-TGN localization of pUL56. In addition, the leucines within C-terminal transmembrane helix were essential for maintaining pUL56 Golgi-TGN retention in cells. Further, the pUL56 can induce downregulation of Golgi-associated protein Rab6a.
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Affiliation(s)
- Chuang Lyu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Haping Road No.678, Xiang Fang District, Harbin, 150069, Heilongjiang, China
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Haping Road No.678, Xiang Fang District, Harbin, 150069, Heilongjiang, China.
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27
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The function of histone acetylation in cervical cancer development. Biosci Rep 2019; 39:BSR20190527. [PMID: 30886064 PMCID: PMC6465204 DOI: 10.1042/bsr20190527] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/19/2022] Open
Abstract
Cervical cancer is the fourth most common female cancer in the world. It is well known that cervical cancer is closely related to high-risk human papillomavirus (HPV) infection. However, epigenetics has increasingly been recognized for its role in tumorigenesis. Epigenetics refers to changes in gene expression levels based on non-gene sequence changes, primarily through transcription or translation of genes regulation, thus affecting its function and characteristics. Typical post-translational modifications (PTMs) include acetylation, propionylation, butyrylation, malonylation and succinylation, among which the acetylation modification of lysine sites has been studied more clearly so far. The acetylation modification of lysine residues in proteins is involved in many aspects of cellular life activities, including carbon metabolism, transcriptional regulation, amino acid metabolism and so on. In this review, we summarize the latest discoveries on cervical cancer development arising from the aspect of acetylation, especially histone acetylation.
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28
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Aksnes H, Ree R, Arnesen T. Co-translational, Post-translational, and Non-catalytic Roles of N-Terminal Acetyltransferases. Mol Cell 2019; 73:1097-1114. [PMID: 30878283 DOI: 10.1016/j.molcel.2019.02.007] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 02/07/2023]
Abstract
Recent studies of N-terminal acetylation have identified new N-terminal acetyltransferases (NATs) and expanded the known functions of these enzymes beyond their roles as ribosome-associated co-translational modifiers. For instance, the identification of Golgi- and chloroplast-associated NATs shows that acetylation of N termini also happens post-translationally. In addition, we now appreciate that some NATs are highly specific; for example, a dedicated NAT responsible for post-translational N-terminal acetylation of actin was recently revealed. Other studies have extended NAT function beyond Nt acetylation, including functions as lysine acetyltransferases (KATs) and non-catalytic roles. Finally, emerging studies emphasize the physiological relevance of N-terminal acetylation, including roles in calorie-restriction-induced longevity and pathological α-synuclein aggregation in Parkinson's disease. Combined, the NATs rise as multifunctional proteins, and N-terminal acetylation is gaining recognition as a major cellular regulator.
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Affiliation(s)
- Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Rasmus Ree
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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29
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Ree R, Varland S, Arnesen T. Spotlight on protein N-terminal acetylation. Exp Mol Med 2018; 50:1-13. [PMID: 30054468 PMCID: PMC6063853 DOI: 10.1038/s12276-018-0116-z] [Citation(s) in RCA: 251] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 01/11/2023] Open
Abstract
N-terminal acetylation (Nt-acetylation) is a widespread protein modification among eukaryotes and prokaryotes alike. By appending an acetyl group to the N-terminal amino group, the charge, hydrophobicity, and size of the N-terminus is altered in an irreversible manner. This alteration has implications for the lifespan, folding characteristics and binding properties of the acetylated protein. The enzymatic machinery responsible for Nt-acetylation has been largely described, but significant knowledge gaps remain. In this review, we provide an overview of eukaryotic N-terminal acetyltransferases (NATs) and the impact of Nt-acetylation. We also discuss other functions of known NATs and outline methods for studying Nt-acetylation. A chemical modification of protein structure called N-terminal acetylation occurs normally in many circumstances, but is also implicated in diseases including cancers and developmental disorders. It adds an acetyl group, composed of a carbonyl group (C = O) linked to a methyl group (CH3), to the nitrogen atom found at one end of a protein chain. Thomas Arnesen at the University of Bergen in Norway and colleagues review the understanding of this modification and survey the enzymes that carry it out. Acetylation occurs on around 80% of human proteins and affects crucial aspects of their function. These include the stability that determines proteins’ lifetimes inside cells, the three-dimensional structures that proteins fold into, and the interactions between different proteins. Advances in analytical techniques are yielding new insights into the role of N-terminal acetylation in health and disease.
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Affiliation(s)
- Rasmus Ree
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Sylvia Varland
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway.,Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway. .,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway. .,Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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30
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Magin RS, Deng S, Zhang H, Cooperman B, Marmorstein R. Probing the interaction between NatA and the ribosome for co-translational protein acetylation. PLoS One 2017; 12:e0186278. [PMID: 29016658 PMCID: PMC5634638 DOI: 10.1371/journal.pone.0186278] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/28/2017] [Indexed: 01/02/2023] Open
Abstract
N-terminal acetylation is among the most abundant protein modifications in eukaryotic cells. Over the last decade, significant progress has been made in elucidating the function of N-terminal acetylation for a number of diverse systems, involved in a wide variety of biological processes. The enzymes responsible for the modification are the N-terminal acetyltransferases (NATs). The NATs are a highly conserved group of enzymes in eukaryotes, which are responsible for acetylating over 80% of the soluble proteome in human cells. Importantly, many of these NATs act co-translationally; they interact with the ribosome near the exit tunnel and acetylate the nascent protein chain as it is being translated. While the structures of many of the NATs have been determined, the molecular basis for the interaction with ribosome is not known. Here, using purified ribosomes and NatA, a very well-studied NAT, we show that NatA forms a stable complex with the ribosome in the absence of other stabilizing factors and through two conserved regions; primarily through an N-terminal domain and an internal basic helix. These regions may orient the active site of the NatA to face the peptide emerging from the exit tunnel. This work provides a framework for understanding how NatA and potentially other NATs interact with the ribosome for co-translational protein acetylation and sets the foundation for future studies to decouple N-terminal acetyltransferase activity from ribosome association.
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Affiliation(s)
- Robert S. Magin
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sunbin Deng
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Haibo Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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