1
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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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Zarges C, Riemer J. Oxidative protein folding in the intermembrane space of human mitochondria. FEBS Open Bio 2024. [PMID: 38867508 DOI: 10.1002/2211-5463.13839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
The mitochondrial intermembrane space hosts a machinery for oxidative protein folding, the mitochondrial disulfide relay. This machinery imports a large number of soluble proteins into the compartment, where they are retained through oxidative folding. Additionally, the disulfide relay enhances the stability of many proteins by forming disulfide bonds. In this review, we describe the mitochondrial disulfide relay in human cells, its components, and their coordinated collaboration in mechanistic detail. We also discuss the human pathologies associated with defects in this machinery and its protein substrates, providing a comprehensive overview of its biological importance and implications for health.
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Affiliation(s)
| | - Jan Riemer
- Institute for Biochemistry, University of Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
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3
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Arnesen T, Kjosås I, McTiernan N. Protein N-terminal acetylation is entering the degradation end game. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00723-1. [PMID: 38519774 DOI: 10.1038/s41580-024-00723-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Affiliation(s)
- Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Ine Kjosås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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4
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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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5
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Gong X, Boyer JB, Gierlich S, Pożoga M, Weidenhausen J, Sinning I, Meinnel T, Giglione C, Wang Y, Hell R, Wirtz M. HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana. Cell Rep 2024; 43:113768. [PMID: 38363676 DOI: 10.1016/j.celrep.2024.113768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
The ribosome-tethered N-terminal acetyltransferase A (NatA) acetylates 52% of soluble proteins in Arabidopsis thaliana. This co-translational modification of the N terminus stabilizes diverse cytosolic plant proteins. The evolutionary conserved Huntingtin yeast partner K (HYPK) facilitates NatA activity in planta, but in vitro, its N-terminal helix α1 inhibits human NatA activity. To dissect the regulatory function of HYPK protein domains in vivo, we genetically engineer CRISPR-Cas9 mutants expressing a HYPK fragment lacking all functional domains (hypk-cr1) or an internally deleted HYPK variant truncating helix α1 but retaining the C-terminal ubiquitin-associated (UBA) domain (hypk-cr2). We find that the UBA domain of HYPK is vital for stabilizing the NatA complex in an organ-specific manner. The N terminus of HYPK, including helix α1, is critical for promoting NatA activity on substrates starting with various amino acids. Consequently, deleting only 42 amino acids inside the HYPK N terminus causes substantial destabilization of the plant proteome and higher tolerance toward drought stress.
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Affiliation(s)
- Xiaodi Gong
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Simone Gierlich
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marlena Pożoga
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yonghong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 271018 Tai'an, China
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany.
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6
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Kong KYE, Shankar S, Rühle F, Khmelinskii A. Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun 2023; 14:8363. [PMID: 38102142 PMCID: PMC10724198 DOI: 10.1038/s41467-023-44096-z] [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: 08/11/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studied, our understanding of C-degrons is still limited. Towards a comprehensive understanding of eukaryotic C-degron pathways, here we perform an unbiased survey of C-degrons in budding yeast. We identify over 5000 potential C-degrons by stability profiling of random peptide libraries and of the yeast C‑terminome. Combining machine learning, high-throughput mutagenesis and genetic screens reveals that the SCF ubiquitin ligase targets ~40% of degrons using a single F-box substrate receptor Das1. Although sequence-specific, Das1 is highly promiscuous, recognizing a variety of C-degron motifs. By screening for full-length substrates, we implicate SCFDas1 in degradation of orphan protein complex subunits. Altogether, this work highlights the variety of C-degron pathways in eukaryotes and uncovers how an SCF/C-degron pathway of broad specificity contributes to proteostasis.
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Affiliation(s)
| | | | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
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7
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Yaguchi T, Kameno M, Taira H, Kawakami J. Mitochondrial Dynamics of Bcl-2 Family Proteins during 17-β-Estradiol-Induced Apoptosis Correlate with the Malignancy of Endometrial Cancer Cells. Biochemistry 2023; 62:3041-3049. [PMID: 37856786 DOI: 10.1021/acs.biochem.3c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Excessive fat intake leads to an increase in cholesterol. Overexposure to estrogen derived from cholesterol is known to contribute to the malignancy of endometrial adenocarcinomas. However, it is not well understood the relationship between the exposure to estrogen and the malignancy of endometrial adenocarcinomas. We investigated how estrogen affected the malignancy of endometrial cancer cells, specifically HEC1 cells (a moderately differentiated adenocarcinoma) and HEC50B cells (a poorly differentiated adenocarcinoma). Cell viability was decreased by exogenous 17-β-estradiol (E2) in a concentration-dependent manner. E2 disturbed the mitochondrial membrane potentials by changing the localization of the B-cell lymphoma 2 (Bcl-2) family protein; however, there were significant differences in the localization of Bcl-2 family proteins between HEC1 and HEC50B cells. In HEC1 cells, E2 increased the expression of B-cell lymphoma-extra large (Bcl-XL) and the Bcl-2-associated X protein (Bax) and decreased Bcl-2 and Bcl-2-associated death promoter (Bad) expression on the outer mitochondrial membrane. Conversely, E2 increased the expression of Bad and Bax, and it decreased Bcl-2 and Bcl-XL expressions on the outer mitochondrial membrane in HEC50B cells. The disturbance of the mitochondrial membrane potential led to the release of cytochrome c from the mitochondria to the cytosolic space followed by activating caspase-9. After that, caspase-3 was activated and induced apoptosis. These results suggested that the localization of the Bcl-2 family protein observed under E2-induced apoptosis is related to the malignancy of endometrial cancer cells. We hope that the dynamics of Bcl-2 family proteins such as Bcl-XL and Bad will be used to diagnose malignant endometrial adenocarcinomas.
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Affiliation(s)
- Takahiro Yaguchi
- Department of Medical Laboratory Science, Graduate School of Health and Welfare Sciences, International University of Health and Welfare, 137-1 Enokizu, Okawa, Fukuoka 831-8501, Japan
| | - Misaki Kameno
- Department of Nanobiochemistry, Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hirofumi Taira
- Department of Medical Laboratory Science, Graduate School of Health and Welfare Sciences, International University of Health and Welfare, 137-1 Enokizu, Okawa, Fukuoka 831-8501, Japan
| | - Junji Kawakami
- Department of Nanobiochemistry, Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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8
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Varland S, Silva RD, Kjosås I, Faustino A, Bogaert A, Billmann M, Boukhatmi H, Kellen B, Costanzo M, Drazic A, Osberg C, Chan K, Zhang X, Tong AHY, Andreazza S, Lee JJ, Nedyalkova L, Ušaj M, Whitworth AJ, Andrews BJ, Moffat J, Myers CL, Gevaert K, Boone C, Martinho RG, Arnesen T. N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity. Nat Commun 2023; 14:6774. [PMID: 37891180 PMCID: PMC10611716 DOI: 10.1038/s41467-023-42342-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Most eukaryotic proteins are N-terminally acetylated, but the functional impact on a global scale has remained obscure. Using genome-wide CRISPR knockout screens in human cells, we reveal a strong genetic dependency between a major N-terminal acetyltransferase and specific ubiquitin ligases. Biochemical analyses uncover that both the ubiquitin ligase complex UBR4-KCMF1 and the acetyltransferase NatC recognize proteins bearing an unacetylated N-terminal methionine followed by a hydrophobic residue. NatC KO-induced protein degradation and phenotypes are reversed by UBR knockdown, demonstrating the central cellular role of this interplay. We reveal that loss of Drosophila NatC is associated with male sterility, reduced longevity, and age-dependent loss of motility due to developmental muscle defects. Remarkably, muscle-specific overexpression of UbcE2M, one of the proteins targeted for NatC KO-mediated degradation, suppresses defects of NatC deletion. In conclusion, NatC-mediated N-terminal acetylation acts as a protective mechanism against protein degradation, which is relevant for increased longevity and motility.
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Affiliation(s)
- Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, N-5006, Bergen, Norway.
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Rui Duarte Silva
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal.
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139, Faro, Portugal.
| | - Ine Kjosås
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway
| | - Alexandra Faustino
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Annelies Bogaert
- VIB-UGent Center for Medical Biotechnology, B-9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, D-53127, Bonn, Germany
| | - Hadi Boukhatmi
- Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1, CNRS, UMR6290, 35065, Rennes, France
| | - Barbara Kellen
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Michael Costanzo
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway
| | - Camilla Osberg
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway
| | - Katherine Chan
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Xiang Zhang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Amy Hin Yan Tong
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Simonetta Andreazza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Juliette J Lee
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Lyudmila Nedyalkova
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Matej Ušaj
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | - Brenda J Andrews
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Jason Moffat
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
| | - Charles Boone
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- RIKEN Centre for Sustainable Resource Science, Wako, Saitama, 351-0106, Japan
| | - Rui Gonçalo Martinho
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal.
- Departmento de Ciências Médicas, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
- iBiMED - Institute of Biomedicine, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, N-5006, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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9
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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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10
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Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen T, Olsen JV. Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. Nat Commun 2023; 14:4517. [PMID: 37500638 PMCID: PMC10374663 DOI: 10.1038/s41467-023-40224-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ~50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employ a multi-dimensional proteomics approach to analyze Saccharomyces cerevisiae lacking NatA activity, which causes global proteome remodeling. Pulsed-SILAC experiments reveals that NatA-deficient strains consistently increase degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovers decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Magnus E Jakobsson
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Biosciences, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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11
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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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12
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Hanna R, Rozenberg A, Saied L, Ben-Yosef D, Lavy T, Kleifeld O. In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation. Mol Cell Proteomics 2023:100584. [PMID: 37236440 PMCID: PMC10362333 DOI: 10.1016/j.mcpro.2023.100584] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases, and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
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Affiliation(s)
- Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Daniel Ben-Yosef
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
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13
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Elurbide J, Carte B, Guedes J, Aldabe R. NatB Catalytic Subunit Depletion Disrupts DNA Replication Initiation Leading to Senescence in MEFs. Int J Mol Sci 2023; 24:ijms24108724. [PMID: 37240070 DOI: 10.3390/ijms24108724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Alpha-aminoterminal acetyltransferase B (NatB) is a critical enzyme responsible for acetylating the aminoterminal end of proteins, thereby modifying approximately 21% of the proteome. This post-translational modification impacts protein folding, structure, stability, and interactions between proteins which, in turn, play a crucial role in modulating several biological functions. NatB has been widely studied for its role in cytoskeleton function and cell cycle regulation in different organisms, from yeast to human tumor cells. In this study, we aimed to understand the biological importance of this modification by inactivating the catalytic subunit of the NatB enzymatic complex, Naa20, in non-transformed mammal cells. Our findings demonstrate that depletion of NAA20 results in decreased cell cycle progression and DNA replication initiation, ultimately leading to the senescence program. Furthermore, we have identified NatB substrates that play a role in cell cycle progression, and their stability is compromised when NatB is inactivated. These results underscore the significance of N-terminal acetylation by NatB in regulating cell cycle progression and DNA replication.
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Affiliation(s)
- Jasmin Elurbide
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Beatriz Carte
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Joana Guedes
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA/UM), University of Minho, 4710-057 Braga, Portugal
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
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14
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van de Kooij B, de Vries E, Rooswinkel RW, Janssen GMC, Kok FK, van Veelen PA, Borst J. N-terminal acetylation can stabilize proteins independent of their ubiquitination. Sci Rep 2023; 13:5333. [PMID: 37005459 PMCID: PMC10067848 DOI: 10.1038/s41598-023-32380-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/27/2023] [Indexed: 04/04/2023] Open
Abstract
The majority of proteins in mammalian cells are modified by covalent attachment of an acetyl-group to the N-terminus (Nt-acetylation). Paradoxically, Nt-acetylation has been suggested to inhibit as well as to promote substrate degradation. Contrasting these findings, proteome-wide stability measurements failed to detect any correlation between Nt-acetylation status and protein stability. Accordingly, by analysis of protein stability datasets, we found that predicted Nt-acetylation positively correlates with protein stability in case of GFP, but this correlation does not hold for the entire proteome. To further resolve this conundrum, we systematically changed the Nt-acetylation and ubiquitination status of model substrates and assessed their stability. For wild-type Bcl-B, which is heavily modified by proteasome-targeting lysine ubiquitination, Nt-acetylation did not correlate with protein stability. For a lysine-less Bcl-B mutant, however, Nt-acetylation correlated with increased protein stability, likely due to prohibition of ubiquitin conjugation to the acetylated N-terminus. In case of GFP, Nt-acetylation correlated with increased protein stability, as predicted, but our data suggest that Nt-acetylation does not affect GFP ubiquitination. Similarly, in case of the naturally lysine-less protein p16, Nt-acetylation correlated with protein stability, regardless of ubiquitination on its N-terminus or on an introduced lysine residue. A direct effect of Nt-acetylation on p16 stability was supported by studies in NatB-deficient cells. Together, our studies argue that Nt-acetylation can stabilize proteins in human cells in a substrate-specific manner, by competition with N-terminal ubiquitination, but also by other mechanisms that are independent of protein ubiquitination status.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands.
| | - Evert de Vries
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Rogier W Rooswinkel
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Frédérique K Kok
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jannie Borst
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands.
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15
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Lundekvam M, Arnesen T, McTiernan N. Using cell lysates to assess N-terminal acetyltransferase activity and impairment. Methods Enzymol 2023; 686:29-43. [PMID: 37532404 DOI: 10.1016/bs.mie.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
The vast majority of eukaryotic proteins are subjected to N-terminal (Nt) acetylation. This reaction is catalyzed by a group of N-terminal acetyltransferases (NATs), which co- or post-translationally transfer an acetyl group from Acetyl coenzyme A to the protein N-terminus. Nt-acetylation plays an important role in many cellular processes, but the functional consequences of this widespread protein modification are still undefined for most proteins. Several in vitro acetylation assays have been developed to study the catalytic activity and substrate specificity of NATs or other acetyltransferases. These assays are valuable tools that can be used to define substrate specificities of yet uncharacterized NAT candidates, assess catalytic impairment of pathogenic NAT variants, and determine the potency of chemical inhibitors. The enzyme input in acetylation assays is typically acetyltransferases that have been recombinantly expressed and purified or immunoprecipitated proteins. In this chapter, we highlight how cell lysates can also be used to assess NAT catalytic activity and impairment when used as input in a previously described isotope-based in vitro Nt-acetylation assay. This is a fast and highly sensitive method that utilizes isotope labeled 14C-Ac-CoA and scintillation to detect the formation of Nt-acetylated peptide products.
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Affiliation(s)
- Malin Lundekvam
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - 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.
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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16
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Müller F, Bange T. Identification of N-degrons and N-recognins using peptide pull-downs combined with quantitative mass spectrometry. Methods Enzymol 2023; 686:67-97. [PMID: 37532409 DOI: 10.1016/bs.mie.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Regulated protein degradation controls protein levels of all short-lived proteins to ensure cellular homeostasis and also protects cells from misfolded or other abnormal proteins. The most important players in the degradation system are E3 ubiquitin ligases which recognize exposed sequence motifs, so-called degrons, of target proteins and mark them through the attachment of ubiquitin for degradation. N-terminal (Nt) sequences are extensively used as degrons (N-degrons) and all 20 amino acids are able to feed proteins in 1 of the 5 known N-degron pathways. Studies have mainly focused on characterizing systematically the role of the starting amino acid on protein stability and less on the identification of the E3 ligases involved. Recent data from our lab and literature suggest that there is an extensive interplay of N-recognins and Nt-modifying enzymes like Nt-acetyltransferases (NATs) or N-myristoyltransferases which only starts to be elucidated. It suggests that improperly modified or unexpectedly unmodified proteins become rapidly removed after synthesis ensuring protein maturation and quality control of specific subsets of proteins. Here, we describe a peptide pull-down and down-stream bioinformatics workflow conducted in the MaxQuant and Perseus computational environment to identify N-recognin candidates in an unbiased way using quantitative mass spectrometry (MS)-based proteomics. Our workflow allows the identification of N-recognin candidates for specific N-degrons, to determine their sequence specificity and it can be applied as well more general to identify binding partners of N-terminal modifications. This method paves the way to identify pathways involved in protein quality control and stability acting at the N-terminus.
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Affiliation(s)
- Franziska Müller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany.
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17
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Ehrmann JF, Grabarczyk DB, Heinke M, Deszcz L, Kurzbauer R, Hudecz O, Shulkina A, Gogova R, Meinhart A, Versteeg GA, Clausen T. Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex. Science 2023; 379:1117-1123. [PMID: 36758105 DOI: 10.1126/science.ade8873] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. The atypical ubiquitin ligase BIRC6 is the only essential IAP, additionally functioning as a suppressor of autophagy. We performed a structure-function analysis of BIRC6 in complex with caspase-9, HTRA2, SMAC, and LC3B, which are critical apoptosis and autophagy proteins. Cryo-electron microscopy structures showed that BIRC6 forms a megadalton crescent shape that arcs around a spacious cavity containing receptor sites for client proteins. Multivalent binding of SMAC obstructs client binding, impeding ubiquitination of both autophagy and apoptotic substrates. On the basis of these data, we discuss how the BIRC6/SMAC complex can act as a stress-induced hub to regulate apoptosis and autophagy drivers.
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Affiliation(s)
- Julian F Ehrmann
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Daniel B Grabarczyk
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Maria Heinke
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Luiza Deszcz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Robert Kurzbauer
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Otto Hudecz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Alexandra Shulkina
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Rebeca Gogova
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Gijs A Versteeg
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Tim Clausen
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
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18
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Zhang J, Qiao W, Luo Y. Mitochondrial quality control proteases and their modulation for cancer therapy. Med Res Rev 2023; 43:399-436. [PMID: 36208112 DOI: 10.1002/med.21929] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 09/04/2022] [Accepted: 09/26/2022] [Indexed: 02/05/2023]
Abstract
Mitochondria, the main provider of energy in eukaryotic cells, contains more than 1000 different proteins and is closely related to the development of cells. However, damaged proteins impair mitochondrial function, further contributing to several human diseases. Evidence shows mitochondrial proteases are critically important for protein maintenance. Most importantly, quality control enzymes exert a crucial role in the modulation of mitochondrial functions by degrading misfolded, aged, or superfluous proteins. Interestingly, cancer cells thrive under stress conditions that damage proteins, so targeting mitochondrial quality control proteases serves as a novel regulator for cancer cells. Not only that, mitochondrial quality control proteases have been shown to affect mitochondrial dynamics by regulating the morphology of optic atrophy 1 (OPA1), which is closely related to the occurrence and progression of cancer. In this review, we introduce mitochondrial quality control proteases as promising targets and related modulators in cancer therapy with a focus on caseinolytic protease P (ClpP), Lon protease (LonP1), high-temperature requirement protein A2 (HrtA2), and OMA-1. Further, we summarize our current knowledge of the advances in clinical trials for modulators of mitochondrial quality control proteases. Overall, the content proposed above serves to suggest directions for the development of novel antitumor drugs.
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Affiliation(s)
- Jiangnan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, Western China Hospital of Sichuan University, Chengdu, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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19
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Arnesen T, Aksnes H, Giglione C. Protein Termini 2022: central roles of protein ends. Trends Biochem Sci 2023; 48:495-499. [PMID: 36997368 DOI: 10.1016/j.tibs.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023]
Abstract
Although locating at the protein ends, N- and C-termini are at the center of numerous cellular functions. This topic engages an increasing number of scientists, recently forming the International Society of Protein Termini (ISPT). Protein Termini 2022 gathered this interdisciplinary community to discuss how protein ends may steer protein functionality.
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20
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Van Damme P, Osberg C, Jonckheere V, Glomnes N, Gevaert K, Arnesen T, Aksnes H. Expanded in vivo substrate profile of the yeast N-terminal acetyltransferase NatC. J Biol Chem 2023; 299:102824. [PMID: 36567016 PMCID: PMC9867985 DOI: 10.1016/j.jbc.2022.102824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
N-terminal acetylation is a conserved protein modification among eukaryotes. The yeast Saccharomyces cerevisiae is a valuable model system for studying this modification. The bulk of protein N-terminal acetylation in S. cerevisiae is catalyzed by the N-terminal acetyltransferases NatA, NatB, and NatC. Thus far, proteome-wide identification of the in vivo protein substrates of yeast NatA and NatB has been performed by N-terminomics. Here, we used S. cerevisiae deleted for the NatC catalytic subunit Naa30 and identified 57 yeast NatC substrates by N-terminal combined fractional diagonal chromatography analysis. Interestingly, in addition to the canonical N-termini starting with ML, MI, MF, and MW, yeast NatC substrates also included MY, MK, MM, MA, MV, and MS. However, for some of these substrate types, such as MY, MK, MV, and MS, we also uncovered (residual) non-NatC NAT activity, most likely due to the previously established redundancy between yeast NatC and NatE/Naa50. Thus, we have revealed a complex interplay between different NATs in targeting methionine-starting N-termini in yeast. Furthermore, our results showed that ectopic expression of human NAA30 rescued known NatC phenotypes in naa30Δ yeast, as well as partially restored the yeast NatC Nt-acetylome. Thus, we demonstrate an evolutionary conservation of NatC from yeast to human thereby underpinning future disease models to study pathogenic NAA30 variants. Overall, this work offers increased biochemical and functional insights into NatC-mediated N-terminal acetylation and provides a basis for future work to pinpoint the specific molecular mechanisms that link the lack of NatC-mediated N-terminal acetylation to phenotypes of NatC deletion yeast.
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Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Camilla Osberg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Veronique Jonckheere
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - 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
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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21
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Bell R, Castellana-Cruz M, Nene A, Thrush RJ, Xu CK, Kumita JR, Vendruscolo M. Effects of N-terminal Acetylation on the Aggregation of Disease-related α-synuclein Variants. J Mol Biol 2023; 435:167825. [PMID: 36099961 DOI: 10.1016/j.jmb.2022.167825] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023]
Abstract
Mutations in the SNCA gene, which encodes the protein α-synuclein, have been linked with early onset Parkinson's disease. The exact nature of this association, however, is still poorly understood. To investigate this problem, we started from the observation that α-synuclein is constitutively N-terminally acetylated, a post-translational modification that alters the charge and structure of α-synuclein molecules and affects their interaction with lipid membranes, as well as their aggregation process. We thus studied five N-terminal acetylated familial variants (A30P, E46K, H50Q, G51D and A53T) of α-synuclein through a wide range of biophysical assays to probe the microscopic steps in their aggregation process and the structures of the resulting aggregates. Our results reveal a great complexity in the combined effects of the disease-related mutations with N-terminal acetylation on the aggregation of α-synuclein, which underscores the great sensitivity to even relatively small perturbations of the behaviour of this protein.
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Affiliation(s)
- Rosie Bell
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Marta Castellana-Cruz
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Aishwarya Nene
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Rebecca J Thrush
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Janet R Kumita
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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22
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Li Y, Zhao Y, Yan X, Ye C, Weirich S, Zhang B, Wang X, Song L, Jiang C, Jeltsch A, Dong C, Mi W. CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation. Nat Commun 2022; 13:7636. [PMID: 36496439 PMCID: PMC9741652 DOI: 10.1038/s41467-022-35169-6] [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: 06/09/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
N-degron pathway plays an important role in the protein quality control and maintenance of cellular protein homeostasis. ZER1 and ZYG11B, the substrate receptors of the Cullin 2-RING E3 ubiquitin ligase (CRL2), recognize N-terminal (Nt) glycine degrons and participate in the Nt-myristoylation quality control through the Gly/N-degron pathway. Here we show that ZER1 and ZYG11B can also recognize small Nt-residues other than glycine. Specifically, ZER1 binds better to Nt-Ser, -Ala, -Thr and -Cys than to -Gly, while ZYG11B prefers Nt-Gly but also has the capacity to recognize Nt-Ser, -Ala and -Cys in vitro. We found that Nt-Ser, -Ala and -Cys undergo Nt-acetylation catalyzed by Nt-acetyltransferase (NAT), thereby shielding them from recognition by ZER1/ZYG11B in cells. Instead, ZER1/ZYG11B readily targets a selection of small Nt-residues lacking Nt-acetylation for degradation in NAT-deficient cells, implicating its role in the Nt-acetylation quality control. Furthermore, we present the crystal structures of ZER1 and ZYG11B bound to various small Nt-residues and uncover the molecular mechanism of non-acetylated substrate recognition by ZER1 and ZYG11B.
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Affiliation(s)
- Yao Li
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Yueling Zhao
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Xiaojie Yan
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Chen Ye
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Sara Weirich
- grid.5719.a0000 0004 1936 9713Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bing Zhang
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Xiaolu Wang
- grid.265021.20000 0000 9792 1228Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070 China
| | - Lili Song
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Chenhao Jiang
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Albert Jeltsch
- grid.5719.a0000 0004 1936 9713Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Cheng Dong
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Wenyi Mi
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
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23
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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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24
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pSNAP: Proteome-wide analysis of elongating nascent polypeptide chains. iScience 2022; 25:104516. [PMID: 35754732 PMCID: PMC9218386 DOI: 10.1016/j.isci.2022.104516] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/10/2022] [Accepted: 05/31/2022] [Indexed: 12/27/2022] Open
Abstract
Cellular global translation is often measured using ribosome profiling or quantitative mass spectrometry, but these methods do not provide direct information at the level of elongating nascent polypeptide chains (NPCs) and associated co-translational events. Here, we describe pSNAP, a method for proteome-wide profiling of NPCs by affinity enrichment of puromycin- and stable isotope-labeled polypeptides. pSNAP does not require ribosome purification and/or chemical labeling, and captures bona fide NPCs that characteristically exhibit protein N-terminus-biased positions. We applied pSNAP to evaluate the effect of silmitasertib, a potential molecular therapy for cancer, and revealed acute translational repression through casein kinase II and mTOR pathways. We also characterized modifications on NPCs and demonstrated that the combination of different types of modifications, such as acetylation and phosphorylation in the N-terminal region of histone H1.5, can modulate interactions with ribosome-associated factors. Thus, pSNAP provides a framework for dissecting co-translational regulations on a proteome-wide scale. Nascent polypeptidome analysis with a simplified protocol Quantification of acute changes in nascent polypeptides induced by external stimuli Profiling and characterization of chemical modifications on nascent polypeptides
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25
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Sindlinger J, Schön S, Eirich J, Kirchgäßner S, Finkemeier I, Schwarzer D. Investigating peptide-Coenzyme A-conjugates as chemical probes for proteomic profiling of N-terminal and lysine acetyltransferases. Chembiochem 2022; 23:e202200255. [PMID: 35776679 PMCID: PMC9541820 DOI: 10.1002/cbic.202200255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/01/2022] [Indexed: 11/18/2022]
Abstract
Acetyl groups are transferred from acetyl‐coenzyme A (Ac‐CoA) to protein N‐termini and lysine side chains by N‐terminal acetyltransferases (NATs) and lysine acetyltransferases (KATs), respectively. Building on lysine‐CoA conjugates as KAT probes, we have synthesized peptide probes with CoA conjugated to N‐terminal alanine (α‐Ala‐CoA), proline (α‐Pro‐CoA) or tri‐glutamic acid (α‐3Glu‐CoA) units for interactome profiling of NAT complexes. The α‐Ala‐CoA probe enriched the majority of NAT catalytic and auxiliary subunits, while a lysine CoA‐conjugate bound only a subset of endogenous KATs. Interactome profiling with the α‐Pro‐CoA probe showed reduced NAT recruitment in favor of metabolic CoA binding proteins and α‐3Glu‐CoA steered the interactome towards NAA80 and NatB. These findings agreed with the inherent substrate specificities of the target proteins and showed that N‐terminal CoA‐conjugated peptides are versatile probes for NAT complex profiling in lysates of physiological and pathological backgrounds.
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Affiliation(s)
- Julia Sindlinger
- Eberhard Karls Universitat Tubingen Mathematisch-Naturwissenschaftliche Fakultat, Interfaculty Institute of Biochemistry, GERMANY
| | - Stefan Schön
- Eberhard Karls Universitat Tubingen Mathematisch-Naturwissenschaftliche Fakultat, Interfakultäres Institut für Biochemie, GERMANY
| | - Jürgen Eirich
- WWU Münster FB 13 Biologie: Westfalische Wilhelms-Universitat Munster Fachbereich 13 Biologie, Institute of Plant Biology and Biotechnology, GERMANY
| | - Sören Kirchgäßner
- Eberhard Karls Universität Tübingen: Eberhard Karls Universitat Tubingen, Interfakultäres Institut für Biochemie, GERMANY
| | - Iris Finkemeier
- WWU Münster FB 13 Biologie: Westfalische Wilhelms-Universitat Munster Fachbereich 13 Biologie, Institute of Plant Biology and Biotechnology, GERMANY
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie Eberhard Karls Universität Tübingen, Chemical Biology, Hoppe-Seyler-Str. 4, 72076, Tübingen, GERMANY
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26
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Zhu L, Lin S, Cui W, Xu Y, Wang L, Wang Z, Yuan S, Zhang Y, Fan Y, Geng J. A nanomedicine enables synergistic chemo/photodynamic therapy for pancreatic cancer treatment. Biomater Sci 2022; 10:3624-3636. [PMID: 35647941 DOI: 10.1039/d2bm00437b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Pancreatic cancer is one of the leading causes of cancer-related deaths worldwide. Gemcitabine (Gem) has been a key chemotherapy agent for pancreatic cancer treatment by suppressing cell proliferation and inducing apoptosis. However, the overexpression of inhibitors of apoptosis (IAP) family of proteins during the carcinogenesis of pancreatic cancer can develop resistance to chemotherapy treatment and result in poor efficacy. To achieve the synergistic combinations of multiple strategies for this dismal disease, we developed a robust nanomedicine system, consisting of a photodynamic therapeutic agent (chlorine e6, Ce6) and a pro-apoptotic peptide-Gem conjugate. To have spatiotemporally controlled drug release, the pro-apoptotic peptide-Gem conjugate was designed to have a vinyldithioether linker that was sensitive to reactive oxygen species (ROS). The nanomedicine was fabricated by the direct self-assembly of the pro-apoptotic peptide-Gem conjugate with Ce6. After being delivered into tumors, the nanomedicine disassembled and rapidly released Gem, Ce6, and the pro-apoptotic peptide upon light illumination (660 nm). Both in vitro and in vivo studies in pancreatic cancer models confirmed the tumor inhibition efficacy with low systemic toxicity to animals.
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Affiliation(s)
- Liwei Zhu
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Shanmeng Lin
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Wenqiang Cui
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youwei Xu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Liang Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Zhaohan Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Shuguang Yuan
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yichuan Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yingfang Fan
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
| | - Jin Geng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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27
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Zhang Z, Xiang S, Cui R, Peng H, Mridul R, Xiang M. ILP-2: A New Bane and Therapeutic Target for Human Cancers. Front Oncol 2022; 12:922596. [PMID: 35814477 PMCID: PMC9260022 DOI: 10.3389/fonc.2022.922596] [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: 04/18/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Inhibitor of apoptosis protein-related-like protein-2 (ILP-2), also known as BIRC-8, is a member of the inhibitor of apoptosis protein (IAPs) family, which mainly encodes the negative regulator of apoptosis. It is selectively overexpressed in a variety of human tumors and can help tumor cells evade apoptosis, promote tumor cell growth, increase tumor cell aggressiveness, and appears to be involved in tumor cell resistance to chemotherapeutic drugs. Several studies have shown that downregulation of ILP-2 expression increases apoptosis, inhibits metastasis, reduces cell growth potential, and sensitizes tumor cells to chemotherapeutic drugs. In addition, ILP-2 inhibits apoptosis in a unique manner; it does not directly inhibit the activity of caspases but induces apoptosis by cooperating with other apoptosis-related proteins. Here, we review the current understanding of the various roles of ILP-2 in the apoptotic cascade and explore the use of interfering ILP-2, and the combination of related anti-tumor agents, as a novel strategy for cancer therapy.
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Affiliation(s)
- Zhiliang Zhang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Siqi Xiang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Ruxia Cui
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Hang Peng
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Roy Mridul
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Mingjun Xiang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
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28
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Miklánková P, Linster E, Boyer JB, Weidenhausen J, Mueller J, Armbruster L, Lapouge K, De La Torre C, Bienvenut W, Sticht C, Mann M, Meinnel T, Sinning I, Giglione C, Hell R, Wirtz M. HYPK promotes the activity of the Nα-acetyltransferase A complex to determine proteostasis of nonAc-X 2/N-degron-containing proteins. SCIENCE ADVANCES 2022; 8:eabn6153. [PMID: 35704578 PMCID: PMC9200280 DOI: 10.1126/sciadv.abn6153] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In humans, the Huntingtin yeast partner K (HYPK) binds to the ribosome-associated Nα-acetyltransferase A (NatA) complex that acetylates ~40% of the proteome in humans and Arabidopsis thaliana. However, the relevance of HsHYPK for determining the human N-acetylome is unclear. Here, we identify the AtHYPK protein as the first in vivo regulator of NatA activity in plants. AtHYPK physically interacts with the ribosome-anchoring subunit of NatA and promotes Nα-terminal acetylation of diverse NatA substrates. Loss-of-AtHYPK mutants are remarkably resistant to drought stress and strongly resemble the phenotype of NatA-depleted plants. The ectopic expression of HsHYPK rescues this phenotype. Combined transcriptomics, proteomics, and N-terminomics unravel that HYPK impairs plant metabolism and development, predominantly by regulating NatA activity. We demonstrate that HYPK is a critical regulator of global proteostasis by facilitating masking of the recently identified nonAc-X2/N-degron. This N-degron targets many nonacetylated NatA substrates for degradation by the ubiquitin-proteasome system.
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Affiliation(s)
- Pavlína Miklánková
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jonas Weidenhausen
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld, 328 Heidelberg, Germany
| | - Johannes Mueller
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld, 328 Heidelberg, Germany
| | - Carolina De La Torre
- Center of Medical Research, Heidelberg University, Theodor-Kutzer-Ufer, Mannheim, Germany
| | - Willy Bienvenut
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carsten Sticht
- Center of Medical Research, Heidelberg University, Theodor-Kutzer-Ufer, Mannheim, Germany
| | - Matthias Mann
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld, 328 Heidelberg, Germany
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, Heidelberg, Germany
- Corresponding author.
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29
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Gibbs DJ, Bailey M, Etherington RD. A stable start: cotranslational Nt-acetylation promotes proteome stability across kingdoms. Trends Cell Biol 2022; 32:374-376. [DOI: 10.1016/j.tcb.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
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30
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Linster E, Forero Ruiz FL, Miklankova P, Ruppert T, Mueller J, Armbruster L, Gong X, Serino G, Mann M, Hell R, Wirtz M. Cotranslational N-degron masking by acetylation promotes proteome stability in plants. Nat Commun 2022; 13:810. [PMID: 35145090 PMCID: PMC8831508 DOI: 10.1038/s41467-022-28414-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
N-terminal protein acetylation (NTA) is a prevalent protein modification essential for viability in animals and plants. The dominant executor of NTA is the ribosome tethered Nα-acetyltransferase A (NatA) complex. However, the impact of NatA on protein fate is still enigmatic. Here, we demonstrate that depletion of NatA activity leads to a 4-fold increase in global protein turnover via the ubiquitin-proteasome system in Arabidopsis. Surprisingly, a concomitant increase in translation, actioned via enhanced Target-of-Rapamycin activity, is also observed, implying that defective NTA triggers feedback mechanisms to maintain steady-state protein abundance. Quantitative analysis of the proteome, the translatome, and the ubiquitome reveals that NatA substrates account for the bulk of this enhanced turnover. A targeted analysis of NatA substrate stability uncovers that NTA absence triggers protein destabilization via a previously undescribed and widely conserved nonAc/N-degron in plants. Hence, the imprinting of the proteome with acetylation marks is essential for coordinating proteome stability. N-terminal protein acetylation is required for plant viability. Here the authors show that reducing N-terminal acetylation by NatA leads to an increase in global protein turnover that is facilitated by absent masking of a novel N-degron
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Francy L Forero Ruiz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas Ruppert
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | | | - Laura Armbruster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Xiaodi Gong
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Giovanna Serino
- Department of Biology and Biotechnology, Sapienza Università di Roma, Rome, Italy
| | - Matthias Mann
- Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany.
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