1
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Klein M, Wild K, Sinning I. Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome. Nat Commun 2024; 15:7681. [PMID: 39227397 PMCID: PMC11372111 DOI: 10.1038/s41467-024-51964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024] Open
Abstract
Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common combination of subsequent modifications carried out on the 80S ribosome. How these enzymatic processes are coordinated in the context of a rapidly translating ribosome has remained elusive. Here, we report two cryo-EM structures of multi-enzyme complexes assembled on vacant human 80S ribosomes, indicating two routes for NME-NTA. Both assemblies form on the 80S independent of nascent chain substrates. Irrespective of the route, NatA occupies a non-intrusive 'distal' binding site on the ribosome which does not interfere with MAP1 or MAP2 binding nor with most other ribosome-associated factors (RAFs). NatA can partake in a coordinated, dynamic assembly with MAP1 through the hydra-like chaperoning function of the abundant Nascent Polypeptide-Associated Complex (NAC). In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Together, our data provide the structural framework for the coordinated orchestration of NME and NTA in protein biogenesis.
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Affiliation(s)
- Marius Klein
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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2
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Lentzsch AM, Yudin D, Gamerdinger M, Chandrasekar S, Rabl L, Scaiola A, Deuerling E, Ban N, Shan SO. NAC guides a ribosomal multienzyme complex for nascent protein processing. Nature 2024:10.1038/s41586-024-07846-7. [PMID: 39169182 DOI: 10.1038/s41586-024-07846-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 07/18/2024] [Indexed: 08/23/2024]
Abstract
Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively1. Both modifications are strictly cotranslational and essential in higher eukaryotic organisms1. The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex2,3 (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K4,5 (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.
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Affiliation(s)
- Alfred M Lentzsch
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Denis Yudin
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Laurenz Rabl
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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3
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Armbruster L, Pożoga M, Wu Z, Eirich J, Thulasi Devendrakumar K, De La Torre C, Miklánková P, Huber M, Bradic F, Poschet G, Weidenhausen J, Merker S, Ruppert T, Sticht C, Sinning I, Finkemeier I, Li X, Hell R, Wirtz M. Nα-acetyltransferase NAA50 mediates plant immunity independent of the Nα-acetyltransferase A complex. PLANT PHYSIOLOGY 2024; 195:3097-3118. [PMID: 38588051 DOI: 10.1093/plphys/kiae200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
In humans and plants, 40% of the proteome is cotranslationally acetylated at the N-terminus by a single Nα-acetyltransferase (Nat) termed NatA. The core NatA complex is comprised of the catalytic subunit Nα-acetyltransferase 10 (NAA10) and the ribosome-anchoring subunit NAA15. The regulatory subunit Huntingtin Yeast Partner K (HYPK) and the acetyltransferase NAA50 join this complex in humans. Even though both are conserved in Arabidopsis (Arabidopsis thaliana), only AtHYPK is known to interact with AtNatA. Here we uncover the AtNAA50 interactome and provide evidence for the association of AtNAA50 with NatA at ribosomes. In agreement with the latter, a split-luciferase approach demonstrated close proximity of AtNAA50 and AtNatA in planta. Despite their interaction, AtNatA/HYPK and AtNAA50 exerted different functions in vivo. Unlike NatA/HYPK, AtNAA50 did not modulate drought tolerance or promote protein stability. Instead, transcriptome and proteome analyses of a novel AtNAA50-depleted mutant (amiNAA50) implied that AtNAA50 negatively regulates plant immunity. Indeed, amiNAA50 plants exhibited enhanced resistance to oomycetes and bacterial pathogens. In contrast to what was observed in NatA-depleted mutants, this resistance was independent of an accumulation of salicylic acid prior to pathogen exposure. Our study dissects the in vivo function of the NatA interactors HYPK and NAA50 and uncovers NatA-independent roles for NAA50 in plants.
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Affiliation(s)
- Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marlena Pożoga
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Zhongshou Wu
- Michael Smith Laboratories, University of British Columbia, V6T1Z4 Vancouver, BC, Canada
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | | | - Carolina De La Torre
- NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Pavlina Miklánková
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Monika Huber
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Fabian Bradic
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jonas Weidenhausen
- Structural Biology, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Sabine Merker
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Ruppert
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University, 69120 Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Irmgard Sinning
- Structural Biology, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, V6T1Z4 Vancouver, BC, Canada
| | - 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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4
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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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5
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Zhu R, Chen M, Luo Y, Cheng H, Zhao Z, Zhang M. The role of N-acetyltransferases in cancers. Gene 2024; 892:147866. [PMID: 37783298 DOI: 10.1016/j.gene.2023.147866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Cancer is a major global health problem that disrupts the balance of normal cellular growth and behavior. Mounting evidence has shown that epigenetic modification, specifically N-terminal acetylation, play a crucial role in the regulation of cell growth and function. Acetylation is a co- or post-translational modification to regulate important cellular progresses such as cell proliferation, cell cycle progress, and energy metabolism. Recently, N-acetyltransferases (NATs), enzymes responsible for acetylation, regulate signal transduction pathway in various cancers including hepatocellular carcinoma, breast cancer, lung cancer, colorectal cancer and prostate cancer. In this review, we clarify the regulatory role of NATs in cancer progression, such as cell proliferation, metastasis, cell apoptosis, autophagy, cell cycle arrest and energy metabolism. Furthermore, the mechanism of NATs on cancer remains to be further studied, and few drugs have been developed. This provides us with a new idea that targeting acetylation, especially NAT-mediated acetylation, may be an attractive way for inhibiting cancer progression.
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Affiliation(s)
- Rongrong Zhu
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Bioinformatics and Medical Big Data, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Mengjiao Chen
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Bioinformatics and Medical Big Data, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Yongjia Luo
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Bioinformatics and Medical Big Data, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China; Department of Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Haipeng Cheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Zhenwang Zhao
- Department of Pathology and Pathophysiology, School of Basic Medicine, Health Science Center, Hubei University of Arts and Science, Xiangyang, Hubei 441053, PR China.
| | - Min Zhang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Department of Bioinformatics and Medical Big Data, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China.
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6
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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: 4] [Impact Index Per Article: 4.0] [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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7
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Chang YH. Impact of Protein N α-Modifications on Cellular Functions and Human Health. Life (Basel) 2023; 13:1613. [PMID: 37511988 PMCID: PMC10381334 DOI: 10.3390/life13071613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Most human proteins are modified by enzymes that act on the α-amino group of a newly synthesized polypeptide. Methionine aminopeptidases can remove the initiator methionine and expose the second amino acid for further modification by enzymes responsible for myristoylation, acetylation, methylation, or other chemical reactions. Specific acetyltransferases can also modify the initiator methionine and sometimes the acetylated methionine can be removed, followed by further modifications. These modifications at the protein N-termini play critical roles in cellular protein localization, protein-protein interaction, protein-DNA interaction, and protein stability. Consequently, the dysregulation of these modifications could significantly change the development and progression status of certain human diseases. The focus of this review is to highlight recent progress in our understanding of the roles of these modifications in regulating protein functions and how these enzymes have been used as potential novel therapeutic targets for various human diseases.
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Affiliation(s)
- Yie-Hwa Chang
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Medical School, Saint Louis, MO 63104, USA
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8
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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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9
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Pan B, Gardner SM, Schultz K, Perez RM, Deng S, Shimogawa M, Sato K, Rhoades E, Marmorstein R, Petersson EJ. Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies. J Am Chem Soc 2023; 145:14019-14030. [PMID: 37319422 PMCID: PMC10728591 DOI: 10.1021/jacs.3c03887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases. A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here, we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes as well as their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Sarah M. Gardner
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kollin Schultz
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryann M. Perez
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Sunbin Deng
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marie Shimogawa
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Kohei Sato
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Elizabeth Rhoades
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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10
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Pan B, Gardner S, Schultz K, Perez RM, Deng S, Shimogawa M, Sato K, Rhoades E, Marmorstein R, Petersson EJ. Semi-synthetic CoA-α-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535351. [PMID: 37066334 PMCID: PMC10104007 DOI: 10.1101/2023.04.03.535351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes and their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
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11
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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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12
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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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13
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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: 5] [Impact Index Per Article: 2.5] [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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Li C, Hu F, Chen H, Zhao J. Transcriptome characteristics during cell wall formation of endosperm cellularization and embryo differentiation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:998664. [PMID: 36262665 PMCID: PMC9575994 DOI: 10.3389/fpls.2022.998664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Embryonic and endosperm development are important biological events during Arabidopsis seed development, and are controlled by dynamic changes in a range of gene expression. Nevertheless, the regulatory mechanisms of endosperm cellularization and embryo differentiation remain unclear. Here, we characterized the early embryo and endosperm development of the naa15 mutant that had abnormal embryo differentiation and incomplete endosperm cellularization compared to WT of Arabidopsis, and comparatively investigated the changes of gene expressions in WT seeds at 3, 4, and 5 days after pollination (3W, 4W, and 5W) and the white homozygous aborted naa15 seeds at 5, 6, and 7 DAP (5M, 6M, and 7M) from naa15-1/+ siliques using RNA sequencing and qPCR assays. The transcriptome analyses showed that there were 2040 and 3630 differentially expressed genes (DEGs) in 4W (at endosperm cellularization initiation stage and heart embryo stage) vs 3W (at syncytium stage and globular embryo stage), and 5W (at end of endosperm cellularization stage and torpedo embryo stage) vs 4W, respectively. The KEGG and GO analyses showed that lipid metabolic processes and transmembrane transport related to cell wall biogenesis, cell division and differentiation, the plant hormone signaling pathway, photosynthesis, and transcription regulator activity were evidently enriched in WT and naa15. The heatmap and qPCR analyses showed that auxin response genes (ARFs), auxin transport genes (PINs) cytokinin synthesis genes (LOGs), cytokinin dehydrogenase genes (CKXs), cytokinin receptor, transcription factors (MYB, bHLH, MADS-box, and ERF) were significantly downregulated in naa15 compared to WT. A series of cell wall genes annotated to xyloglucan endotransglycosylase/hydrolase, pectin methyl esterase, and pectin methyl esterase inhibitor were also identified in these DEGs. Moreover, using an immunofluorescent assay, the features of cell walls displayed that cellulose fluorescence signals in the embryo and endosperm of naa15 were significantly decreased, and the signals of low- and high- methyl esterification of pectin were also obviously decreased in the endosperm of naa15. In summary, we identified a large number of DEGs and investigated the features of cell walls during endosperm cellularization and embryonic differentiation, which provided important information on transcription and gene expression to reveal their regulatory mechanisms.
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15
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Weidenhausen J, Kopp J, Ruger-Herreros C, Stein F, Haberkant P, Lapouge K, Sinning I. Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity. Int J Mol Sci 2022; 23:ijms231810805. [PMID: 36142717 PMCID: PMC9500918 DOI: 10.3390/ijms231810805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most eukaryotic proteins are N-terminally acetylated by a set of Nα acetyltransferases (NATs). This ancient and ubiquitous modification plays a fundamental role in protein homeostasis, while mutations are linked to human diseases and phenotypic defects. In particular, Naa50 features species-specific differences, as it is inactive in yeast but active in higher eukaryotes. Together with NatA, it engages in NatE complex formation for cotranslational acetylation. Here, we report Naa50 homologs from the filamentous fungi Chaetomium thermophilum and Neurospora crassa with significant N- and C-terminal extensions to the conserved GNAT domain. Structural and biochemical analyses show that CtNaa50 shares the GNAT structure and substrate specificity with other homologs. However, in contrast to previously analyzed Naa50 proteins, it does not form NatE. The elongated N-terminus increases Naa50 thermostability and binds to dynein light chain protein 1, while our data suggest that conserved positive patches in the C-terminus allow for ribosome binding independent of NatA. Our study provides new insights into the many facets of Naa50 and highlights the diversification of NATs during evolution.
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Affiliation(s)
- Jonas Weidenhausen
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Carmen Ruger-Herreros
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Center for Molecular Biology of the University of Heidelberg (ZMBH), 69120 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Correspondence:
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16
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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: 14] [Impact Index Per Article: 7.0] [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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17
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Opening opportunities for K d determination and screening of MHC peptide complexes. Commun Biol 2022; 5:488. [PMID: 35606511 PMCID: PMC9127112 DOI: 10.1038/s42003-022-03366-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/13/2022] [Indexed: 01/15/2023] Open
Abstract
An essential element of adaptive immunity is selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes. Using native mass spectrometry, we analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule and, due to its unique stability, we determine binding affinities of complexes loaded with truncated or charge-reduced peptides. We find that the two anchor positions can be stabilized independently, and we further analyze the contribution of additional amino acid positions to the binding strength. As a complement to computational prediction tools, our method estimates binding strength of even low-affinity peptides to MHC class I complexes quickly and efficiently. It has huge potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases, autoimmunity, vaccine design, and cancer immunotherapy. The authors present a sensitive and rapid method to determine the binding strength of MHC class 1 peptide complexes using native mass spectrometry.
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18
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Hydroxylation of the Acetyltransferase NAA10 Trp38 Is Not an Enzyme-Switch in Human Cells. Int J Mol Sci 2021; 22:ijms222111805. [PMID: 34769235 PMCID: PMC8583962 DOI: 10.3390/ijms222111805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
NAA10 is a major N-terminal acetyltransferase (NAT) that catalyzes the cotranslational N-terminal (Nt-) acetylation of 40% of the human proteome. Several reports of lysine acetyltransferase (KAT) activity by NAA10 exist, but others have not been able to find any NAA10-derived KAT activity, the latter of which is supported by structural studies. The KAT activity of NAA10 towards hypoxia-inducible factor 1α (HIF-1α) was recently found to depend on the hydroxylation at Trp38 of NAA10 by factor inhibiting HIF-1α (FIH). In contrast, we could not detect hydroxylation of Trp38 of NAA10 in several human cell lines and found no evidence that NAA10 interacts with or is regulated by FIH. Our data suggest that NAA10 Trp38 hydroxylation is not a switch in human cells and that it alters its catalytic activity from a NAT to a KAT.
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19
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Kweon HY, Lee MN, Dorfel M, Seo S, Gottlieb L, PaPazyan T, McTiernan N, Ree R, Bolton D, Garcia A, Flory M, Crain J, Sebold A, Lyons S, Ismail A, Marchi E, Sonn SK, Jeong SJ, Jeon S, Ju S, Conway SJ, Kim T, Kim HS, Lee C, Roh TY, Arnesen T, Marmorstein R, Oh GT, Lyon GJ. Naa12 compensates for Naa10 in mice in the amino-terminal acetylation pathway. eLife 2021; 10:e65952. [PMID: 34355692 PMCID: PMC8376253 DOI: 10.7554/elife.65952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 08/05/2021] [Indexed: 01/17/2023] Open
Abstract
Amino-terminal acetylation is catalyzed by a set of N-terminal acetyltransferases (NATs). The NatA complex (including X-linked Naa10 and Naa15) is the major acetyltransferase, with 40-50% of all mammalian proteins being potential substrates. However, the overall role of amino-terminal acetylation on a whole-organism level is poorly understood, particularly in mammals. Male mice lacking Naa10 show no globally apparent in vivo amino-terminal acetylation impairment and do not exhibit complete embryonic lethality. Rather Naa10 nulls display increased neonatal lethality, and the majority of surviving undersized mutants exhibit a combination of hydrocephaly, cardiac defects, homeotic anterior transformation, piebaldism, and urogenital anomalies. Naa12 is a previously unannotated Naa10-like paralog with NAT activity that genetically compensates for Naa10. Mice deficient for Naa12 have no apparent phenotype, whereas mice deficient for Naa10 and Naa12 display embryonic lethality. The discovery of Naa12 adds to the currently known machinery involved in amino-terminal acetylation in mice.
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Affiliation(s)
- Hyae Yon Kweon
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Mi-Ni Lee
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
- Laboratory Animal Resource Center Korea ResearchInstitute of Bioscience and BiotechnologyChungbukRepublic of Korea
| | - Max Dorfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Seungwoon Seo
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Leah Gottlieb
- Department of Chemistry, University of PennsylvaniaPhiladelphiaUnited States
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Thomas PaPazyan
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Nina McTiernan
- Department of Biomedicine, University of BergenBergenNorway
| | - Rasmus Ree
- Department of Biomedicine, University of BergenBergenNorway
| | - David Bolton
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Andrew Garcia
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Michael Flory
- Research Design and Analysis Service, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Alison Sebold
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Ahmed Ismail
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Seong-keun Sonn
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Se-Jin Jeong
- Center for Cardiovascular Research, Washington University School of MedicineSaint LouisUnited States
| | - Sejin Jeon
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and TechnologySeoulRepublic of Korea
| | - Simon J Conway
- Herman B. Wells Center for Pediatric Research, Indiana University School of MedicineIndianapolisUnited States
| | - Taesoo Kim
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Hyun-Seok Kim
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and TechnologySeoulRepublic of Korea
- Department of Converging Science and Technology, KHU-KIST, Kyung Hee UniversitySeoulRepublic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and TechnologyPohangRepublic of Korea
| | - Thomas Arnesen
- Department of Biomedicine, University of BergenBergenNorway
- Department of Biological Sciences, University of BergenBergenNorway
- Department of Surgery, Haukeland University HospitalBergenNorway
| | - Ronen Marmorstein
- Department of Chemistry, University of PennsylvaniaPhiladelphiaUnited States
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Goo Taeg Oh
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
- Biology PhD Program, The Graduate Center, The City University of New YorkNew YorkUnited States
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
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20
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Gogoll L, Steindl K, Joset P, Zweier M, Baumer A, Gerth-Kahlert C, Tutschek B, Rauch A. Confirmation of Ogden syndrome as an X-linked recessive fatal disorder due to a recurrent NAA10 variant and review of the literature. Am J Med Genet A 2021; 185:2546-2560. [PMID: 34075687 PMCID: PMC8361982 DOI: 10.1002/ajmg.a.62351] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/07/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
Ogden syndrome is a rare lethal X‐linked recessive disorder caused by a recurrent missense variant (Ser37Pro) in the NAA10 gene, encoding the catalytic subunit of the N‐terminal acetyltransferase A complex (NatA). So far eight boys of two different families have been described in the literature, all presenting the distinctive and recognizable phenotype, which includes mostly postnatal growth retardation, global severe developmental delay, characteristic craniofacial features, and structural cardiac anomalies and/or arrhythmias. Here, we report the ninth case of Ogden syndrome with an independent recurrence of the Ser37Pro variant. We were able to follow the clinical course of the affected boy and delineate the evolving phenotype from his birth until his unfortunate death at 7 months. We could confirm the associated phenotype as well as the natural history of this severe disease. By describing new presenting features, we are further expanding the clinical spectrum associated with Ogden syndrome and review other phenotypes associated with NAA10 variants.
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Affiliation(s)
- Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | | | - Boris Tutschek
- Prenatal Zürich, Zürich, Switzerland.,Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland.,University Children's Hospital, Zurich, Switzerland
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21
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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22
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Bhaskar V, Desogus J, Graff-Meyer A, Schenk AD, Cavadini S, Chao JA. Dynamic association of human Ebp1 with the ribosome. RNA (NEW YORK, N.Y.) 2021; 27:411-419. [PMID: 33479117 PMCID: PMC7962488 DOI: 10.1261/rna.077602.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/02/2021] [Indexed: 05/09/2023]
Abstract
Ribosomes are the macromolecular machines at the heart of protein synthesis; however, their function can be modulated by a variety of additional protein factors that directly interact with them. Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome, and this binding is enhanced upon puromycin-mediated translational inhibition. The association of Ebp1 with the 80S ribosome centers around its interaction with ribosomal proteins eL19 and uL23 and the 28S rRNA. Further analysis of the Ebp1-ribosome complex suggests that Ebp1 can rotate around its insert domain, which may enable it to assume a wide range of conformations while maintaining its interaction with the ribosome. Structurally, Ebp1 shares homology with the methionine aminopeptidase 2 family of enzymes; therefore, this inherent flexibility may also be conserved.
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Affiliation(s)
- Varun Bhaskar
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jessica Desogus
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | | | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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23
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Ward T, Tai W, Morton S, Impens F, Van Damme P, Van Haver D, Timmerman E, Venturini G, Zhang K, Jang MY, Willcox JAL, Haghighi A, Gelb BD, Chung WK, Goldmuntz E, Porter GA, Lifton RP, Brueckner M, Yost HJ, Bruneau BG, Gorham J, Kim Y, Pereira A, Homsy J, Benson CC, DePalma SR, Varland S, Chen CS, Arnesen T, Gevaert K, Seidman C, Seidman JG. Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency. Circ Res 2021; 128:1156-1169. [PMID: 33557580 PMCID: PMC8048381 DOI: 10.1161/circresaha.120.316966] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tarsha Ward
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Warren Tai
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sarah Morton
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Newborn Medicine, Boston Children's Hospital (S.M.)
| | - Francis Impens
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Biochemistry and Microbiology (P.V.D.), Ghent University, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Gabriela Venturini
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,University of Sao Paulo (G.V.)
| | - Kehan Zhang
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Min Young Jang
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jon A L Willcox
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Alireza Haghighi
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - Bruce D Gelb
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York (B.D.G.)
| | - Wendy K Chung
- Pediatrics and Medicine, Columbia University Medical Center, New York (W.K.C.)
| | - Elizabeth Goldmuntz
- Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.)
| | | | - Richard P Lifton
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Laboratory of Human Genetics and Genomics, Rockefeller University, New York (R.P.L.)
| | - Martina Brueckner
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Pediatrics, Yale University School of Medicine, New Haven (M.B.)
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah, Salt Lake City (H.J.Y.)
| | | | - Joshua Gorham
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Yuri Kim
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Cardiovascular Medicine, Brigham and Women's Hospital (Y.K.)
| | - Alexandre Pereira
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jason Homsy
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Craig C Benson
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Steven R DePalma
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sylvia Varland
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada (S.V.)
| | - Christopher S Chen
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Thomas Arnesen
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Surgery, Haukeland University Hospital, N-5021 Bergen, Norway (T.A.)
| | - Kris Gevaert
- Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Christine Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - J G Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
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24
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McTiernan N, Gill H, Prada CE, Pachajoa H, Lores J, Arnesen T. NAA10 p.(N101K) disrupts N-terminal acetyltransferase complex NatA and is associated with developmental delay and hemihypertrophy. Eur J Hum Genet 2021; 29:280-288. [PMID: 32973342 PMCID: PMC7868364 DOI: 10.1038/s41431-020-00728-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 01/23/2023] Open
Abstract
Nearly half of all human proteins are acetylated at their N-termini by the NatA N-terminal acetyltransferase complex. NAA10 is evolutionarily conserved as the catalytic subunit of NatA in complex with NAA15, but may also have NatA-independent functions. Several NAA10 variants are associated with genetic disorders. The phenotypic spectrum includes developmental delay, intellectual disability, and cardiac abnormalities. Here, we have identified the previously undescribed NAA10 c.303C>A and c.303C>G p.(N101K) variants in two unrelated girls. These girls have developmental delay, but they both also display hemihypertrophy a feature normally not observed or registered among these cases. Functional studies revealed that NAA10 p.(N101K) is completely impaired in its ability to bind NAA15 and to form an enzymatically active NatA complex. In contrast, the integrity of NAA10 p.(N101K) as a monomeric acetyltransferase is intact. Thus, this NAA10 variant may represent the best example of the impact of NatA mediated N-terminal acetylation, isolated from other potential NAA10-mediated cellular functions and may provide important insights into the phenotypes observed in individuals expressing pathogenic NAA10 variants.
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Affiliation(s)
- Nina McTiernan
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Harinder Gill
- Department of Medical Genetics, Children's and Women's Health Centre of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Carlos E Prada
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 45229, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
- Centro de Medicina Genomica y Metabolismo, Fundacion Cardiovascular de Colombia, Floridablanca, Colombia
| | - Harry Pachajoa
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras Universidad Icesi, Cali, Colombia
- Fundación Clínica Valle del Lili, Cali, Colombia
| | - Juliana Lores
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras Universidad Icesi, Cali, Colombia
- Fundación Clínica Valle del Lili, Cali, Colombia
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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25
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N α-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae. Cell Rep 2021; 34:108711. [PMID: 33535049 DOI: 10.1016/j.celrep.2021.108711] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 10/10/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022] Open
Abstract
N-terminal (Nt) acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt acetyltransferases (Nats) with differing specificities. Nt acetylation has been implicated in protein quality control, but its broad biological significance remains elusive. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAΔ and natBΔ mutants. Our results reveal a range of NatA- and NatB-specific phenotypes. NatA is implicated in systemic adaptation control, because natAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes, and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, because natBΔ mutants, to a greater extent than natA mutants, accumulate protein aggregates, induce stress responses, and display reduced fitness in the absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.
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26
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Rodríguez-Galán O, García-Gómez JJ, Rosado IV, Wei W, Méndez-Godoy A, Pillet B, Alekseenko A, Steinmetz L, Pelechano V, Kressler D, de la Cruz J. A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Nucleic Acids Res 2021; 49:206-220. [PMID: 33330942 PMCID: PMC7797049 DOI: 10.1093/nar/gkaa1200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/18/2020] [Accepted: 12/14/2020] [Indexed: 12/03/2022] Open
Abstract
Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5' region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.
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Affiliation(s)
- Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Juan J García-Gómez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Iván V Rosado
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Alfonso Méndez-Godoy
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, School of Medicine, Stanford, CA, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
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27
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Structural basis of Naa20 activity towards a canonical NatB substrate. Commun Biol 2021; 4:2. [PMID: 33398031 PMCID: PMC7782713 DOI: 10.1038/s42003-020-01546-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023] Open
Abstract
N-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.
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28
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Weidenhausen J, Kopp J, Armbruster L, Wirtz M, Lapouge K, Sinning I. Structural and functional characterization of the N-terminal acetyltransferase Naa50. Structure 2021; 29:413-425.e5. [PMID: 33400917 DOI: 10.1016/j.str.2020.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 10/22/2022]
Abstract
The majority of eukaryotic proteins is modified by N-terminal acetylation, which plays a fundamental role in protein homeostasis, localization, and complex formation. N-terminal acetyltransferases (NATs) mainly act co-translationally on newly synthesized proteins at the ribosomal tunnel exit. NatA is the major NAT consisting of Naa10 catalytic and Naa15 auxiliary subunits, and with Naa50 forms the NatE complex. Naa50 has recently been identified in Arabidopsis thaliana and is important for plant development and stress response regulation. Here, we determined high-resolution X-ray crystal structures of AtNaa50 in complex with AcCoA and a bisubstrate analog. We characterized its substrate specificity, determined its enzymatic parameters, and identified functionally important residues. Even though Naa50 is conserved among species, we highlight differences between Arabidopsis and yeast, where Naa50 is catalytically inactive but binds CoA conjugates. Our study provides insights into Naa50 conservation, species-specific adaptations, and serves as a basis for further studies of NATs in plants.
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Affiliation(s)
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
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29
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Krtenic B, Drazic A, Arnesen T, Reuter N. Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PLoS Comput Biol 2020; 16:e1007988. [PMID: 33362253 PMCID: PMC7790372 DOI: 10.1371/journal.pcbi.1007988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 01/07/2021] [Accepted: 10/16/2020] [Indexed: 11/19/2022] Open
Abstract
The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases. Enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily transfer an acetyl group from one molecule to another. This reaction is called acetylation and is one of the most common reactions inside the cell. The GNAT superfamily counts more than 870 000 members through all kingdoms of life. Despite sharing the same fold the GNAT superfamily is very diverse in terms of amino acid sequence and substrates. The eight N-terminal acetyltransferases (NatA, NatB, etc.. to NatH) are a GNAT subtype which acetylates the free amine group of polypeptide chains. This modification is called N-terminal acetylation and is one of the most abundant protein modifications in eukaryotic cells. This subtype is also characterized by a high sequence diversity even though they share the same substrate. In addition, the phylogeny of the superfamily is not characterized. This hampers functional annotation based on sequence similarity, and discovery of novel NATs. In this work we set out to solve the problem of the classification of eukaryotic GCN5-related acetyltransferases and report the first classification framework of the superfamily. This framework can be used as a tool for annotation of all GCN5-related acetyltransferases. As an example of what can be achieved we report in this paper the computational prediction and in vitro verification of the function of two previously uncharacterized N-terminal acetyltransferases. We also report the first acetyltransferase phylogenetic tree of the GCN5 superfamily. It indicates that N-terminal acetyltransferases do not constitute one homogeneous protein family, but that the ability to bind and acetylate protein N-termini had evolved more than once on the same acetylation scaffold. We also show that even small changes in key positions can lead to altered enzyme specificity.
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Affiliation(s)
- Bojan Krtenic
- Department of Biological Sciences, University of Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- * E-mail: (BK); (NR)
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, Norway
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Norway
- Department of Biomedicine, University of Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- Department of Chemistry, University of Bergen, Norway
- * E-mail: (BK); (NR)
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30
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Ree R, Kind L, Kaziales A, Varland S, Dai M, Richter K, Drazic A, Arnesen T. PFN2 and NAA80 cooperate to efficiently acetylate the N-terminus of actin. J Biol Chem 2020; 295:16713-16731. [PMID: 32978259 PMCID: PMC7864067 DOI: 10.1074/jbc.ra120.015468] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/22/2020] [Indexed: 12/01/2022] Open
Abstract
The actin cytoskeleton is of profound importance to cell shape, division, and intracellular force generation. Profilins bind to globular (G-)actin and regulate actin filament formation. Although profilins are well-established actin regulators, the distinct roles of the dominant profilin, profilin 1 (PFN1), versus the less abundant profilin 2 (PFN2) remain enigmatic. In this study, we use interaction proteomics to discover that PFN2 is an interaction partner of the actin N-terminal acetyltransferase NAA80, and further confirm this by analytical ultracentrifugation. Enzyme assays with NAA80 and different profilins demonstrate that PFN2 binding specifically increases the intrinsic catalytic activity of NAA80. NAA80 binds PFN2 through a proline-rich loop, deletion of which abrogates PFN2 binding. Small-angle X-ray scattering shows that NAA80, actin, and PFN2 form a ternary complex and that NAA80 has partly disordered regions in the N-terminus and the proline-rich loop, the latter of which is partly ordered upon PFN2 binding. Furthermore, binding of PFN2 to NAA80 via the proline-rich loop promotes binding between the globular domains of actin and NAA80, and thus acetylation of actin. However, the majority of cellular NAA80 is stably bound to PFN2 and not to actin, and we propose that this complex acetylates G-actin before it is incorporated into filaments. In conclusion, we reveal a functionally specific role of PFN2 as a stable interactor and regulator of the actin N-terminal acetyltransferase NAA80, and establish the modus operandi for NAA80-mediated actin N-terminal acetylation, a modification with a major impact on cytoskeletal dynamics.
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Affiliation(s)
- Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Anna Kaziales
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Sylvia Varland
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Minglu Dai
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Klaus Richter
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Adrian Drazic
- 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
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31
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NAA10 p.(D10G) and NAA10 p.(L11R) Variants Hamper Formation of the NatA N-Terminal Acetyltransferase Complex. Int J Mol Sci 2020; 21:ijms21238973. [PMID: 33255974 PMCID: PMC7730585 DOI: 10.3390/ijms21238973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 11/21/2022] Open
Abstract
The majority of the human proteome is subjected to N-terminal (Nt) acetylation catalysed by N-terminal acetyltransferases (NATs). The NatA complex is composed of two core subunits—the catalytic subunit NAA10 and the ribosomal anchor NAA15. Furthermore, NAA10 may also have catalytic and non-catalytic roles independent of NatA. Several inherited and de novo NAA10 variants have been associated with genetic disease in humans. In this study, we present a functional analysis of two de novo NAA10 variants, c.29A>G p.(D10G) and c.32T>G p.(L11R), previously identified in a male and a female, respectively. Both of these neighbouring amino acids are highly conserved in NAA10. Immunoprecipitation experiments revealed that both variants hamper complex formation with NAA15 and are thus likely to impair NatA-mediated Nt-acetylation in vivo. Despite their common impact on NatA formation, in vitro Nt-acetylation assays showed that the variants had opposing impacts on NAA10 catalytic activity. While NAA10 c.29A>G p.(D10G) exhibits normal intrinsic NatA activity and reduced monomeric NAA10 NAT activity, NAA10 c.32T>G p.(L11R) displays reduced NatA activity and normal NAA10 NAT activity. This study expands the scope of research into the functional consequences of NAA10 variants and underlines the importance of understanding the diverse cellular roles of NAA10 in disease mechanisms.
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32
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Grunwald S, Hopf LVM, Bock-Bierbaum T, Lally CCM, Spahn CMT, Daumke O. Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates. Nat Commun 2020; 11:5506. [PMID: 33139728 PMCID: PMC7608589 DOI: 10.1038/s41467-020-19321-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
The heterotrimeric NatC complex, comprising the catalytic Naa30 and the two auxiliary subunits Naa35 and Naa38, co-translationally acetylates the N-termini of numerous eukaryotic target proteins. Despite its unique subunit composition, its essential role for many aspects of cellular function and its suggested involvement in disease, structure and mechanism of NatC have remained unknown. Here, we present the crystal structure of the Saccharomyces cerevisiae NatC complex, which exhibits a strikingly different architecture compared to previously described N-terminal acetyltransferase (NAT) complexes. Cofactor and ligand-bound structures reveal how the first four amino acids of cognate substrates are recognized at the Naa30–Naa35 interface. A sequence-specific, ligand-induced conformational change in Naa30 enables efficient acetylation. Based on detailed structure–function studies, we suggest a catalytic mechanism and identify a ribosome-binding patch in an elongated tip region of NatC. Our study reveals how NAT machineries have divergently evolved to N-terminally acetylate specific subsets of target proteins. The conserved eukaryotic heterotrimeric NatC complex co-translationally acetylates the N-termini of numerous target proteins. Here, the authors provide insights into the catalytic mechanism of NatC by determining the crystal structures of Saccharomyces cerevisiae NatC in the absence and presence of cofactors and peptide substrates and reveal the molecular basis of substrate binding by further biochemical analyses.
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Affiliation(s)
- Stephan Grunwald
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Linus V M Hopf
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tobias Bock-Bierbaum
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Ciara C M Lally
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Oliver Daumke
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany. .,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
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33
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Ritter A, Berger JH, Deardorff M, Izumi K, Lin KY, Medne L, Ahrens-Nicklas RC. Variants in NAA15 cause pediatric hypertrophic cardiomyopathy. Am J Med Genet A 2020; 185:228-233. [PMID: 33103328 DOI: 10.1002/ajmg.a.61928] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 01/28/2023]
Abstract
The NatA N-acetyltransferase complex is important for cotranslational protein modification and regulation of multiple cellular processes. The NatA complex includes the core components of NAA10, the catalytic subunit, and NAA15, the auxiliary component. Both NAA10 and NAA15 have been associated with neurodevelopmental disorders with overlapping clinical features, including variable intellectual disability, dysmorphic facial features, and, less commonly, congenital anomalies such as cleft lip or palate. Cardiac arrhythmias, including long QT syndrome, ventricular tachycardia, and ventricular fibrillation were among the first reported cardiac manifestations in patients with NAA10-related syndrome. Recently, three individuals with NAA10-related syndrome have been reported to also have hypertrophic cardiomyopathy (HCM). The general and cardiac phenotypes of NAA15-related syndrome are not as well described as NAA10-related syndrome. Congenital heart disease, including ventricular septal defects, and arrhythmias, such as ectopic atrial tachycardia, have been reported in a small proportion of patients with NAA15-related syndrome. Given the relationship between NAA10 and NAA15, we propose that HCM is also likely to occur in NAA15-related disorder. We present two patients with pediatric HCM found to have NAA15-related disorder via exome sequencing, providing the first evidence that variants in NAA15 can cause HCM.
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Affiliation(s)
- Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin H Berger
- Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Deardorff
- Department of Pathology and Laboratory Medicine and Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kimberly Y Lin
- Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Livija Medne
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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34
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Linster E, Layer D, Bienvenut WV, Dinh TV, Weyer FA, Leemhuis W, Brünje A, Hoffrichter M, Miklankova P, Kopp J, Lapouge K, Sindlinger J, Schwarzer D, Meinnel T, Finkemeier I, Giglione C, Hell R, Sinning I, Wirtz M. The Arabidopsis N α -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response. THE NEW PHYTOLOGIST 2020; 228:554-569. [PMID: 32548857 DOI: 10.1111/nph.16747] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In humans and plants, N-terminal acetylation plays a central role in protein homeostasis, affects 80% of proteins in the cytoplasm and is catalyzed by five ribosome-associated N-acetyltransferases (NatA-E). Humans also possess a Golgi-associated NatF (HsNAA60) that is essential for Golgi integrity. Remarkably, NAA60 is absent in fungi and has not been identified in plants. Here we identify and characterize the first plasma membrane-anchored post-translationally acting N-acetyltransferase AtNAA60 in the reference plant Arabidopsis thaliana by the combined application of reverse genetics, global proteomics, live-cell imaging, microscale thermophoresis, circular dichroism spectroscopy, nano-differential scanning fluorometry, intrinsic tryptophan fluorescence and X-ray crystallography. We demonstrate that AtNAA60, like HsNAA60, is membrane-localized in vivo by an α-helical membrane anchor at its C-terminus, but in contrast to HsNAA60, AtNAA60 localizes to the plasma membrane. The AtNAA60 crystal structure provides insights into substrate-binding, the broad substrate specificity and the catalytic mechanism probed by structure-based mutagenesis. Characterization of the NAA60 loss-of-function mutants (naa60-1 and naa60-2) uncovers a plasma membrane-localized substrate of AtNAA60 and the importance of NAA60 during high salt stress. Our findings provide evidence for the plant-specific evolution of a plasma membrane-anchored N-acetyltransferase that is vital for adaptation to stress.
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Dominik Layer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Trinh V Dinh
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Felix A Weyer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Wiebke Leemhuis
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Marion Hoffrichter
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Ruediger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
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35
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Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation. Trends Biochem Sci 2020; 46:15-27. [PMID: 32912665 DOI: 10.1016/j.tibs.2020.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022]
Abstract
N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.
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36
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Deng S, Pan B, Gottlieb L, Petersson EJ, Marmorstein R. Molecular basis for N-terminal alpha-synuclein acetylation by human NatB. eLife 2020; 9:57491. [PMID: 32885784 PMCID: PMC7494357 DOI: 10.7554/elife.57491] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022] Open
Abstract
NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and Candida albicans NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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37
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Armbruster L, Linster E, Boyer JB, Brünje A, Eirich J, Stephan I, Bienvenut WV, Weidenhausen J, Meinnel T, Hell R, Sinning I, Finkemeier I, Giglione C, Wirtz M. NAA50 Is an Enzymatically Active N α-Acetyltransferase That Is Crucial for Development and Regulation of Stress Responses. PLANT PHYSIOLOGY 2020; 183:1502-1516. [PMID: 32461302 PMCID: PMC7401105 DOI: 10.1104/pp.20.00222] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/15/2020] [Indexed: 05/11/2023]
Abstract
Nα-terminal acetylation (NTA) is a prevalent protein modification in eukaryotes. In plants, the biological function of NTA remains enigmatic. The dominant N-acetyltransferase (Nat) in Arabidopsis (Arabidopsis thaliana) is NatA, which cotranslationally catalyzes acetylation of ∼40% of the proteome. The core NatA complex consists of the catalytic subunit NAA10 and the ribosome-anchoring subunit NAA15. In human (Homo sapiens), fruit fly (Drosophila melanogaster), and yeast (Saccharomyces cerevisiae), this core NatA complex interacts with NAA50 to form the NatE complex. While in metazoa, NAA50 has N-acetyltransferase activity, yeast NAA50 is catalytically inactive and positions NatA at the ribosome tunnel exit. Here, we report the identification and characterization of Arabidopsis NAA50 (AT5G11340). Consistent with its putative function as a cotranslationally acting Nat, AtNAA50-EYFP localized to the cytosol and the endoplasmic reticulum but also to the nuclei. We demonstrate that purified AtNAA50 displays Nα-terminal acetyltransferase and lysine-ε-autoacetyltransferase activity in vitro. Global N-acetylome profiling of Escherichia coli cells expressing AtNAA50 revealed conservation of NatE substrate specificity between plants and humans. Unlike the embryo-lethal phenotype caused by the absence of AtNAA10 and AtNAA15, loss of NAA50 expression resulted in severe growth retardation and infertility in two Arabidopsis transfer DNA insertion lines (naa50-1 and naa50-2). The phenotype of naa50-2 was rescued by the expression of HsNAA50 or AtNAA50. In contrast, the inactive ScNAA50 failed to complement naa50-2 Remarkably, loss of NAA50 expression did not affect NTA of known NatA substrates and caused the accumulation of proteins involved in stress responses. Overall, our results emphasize a relevant role of AtNAA50 in plant defense and development, which is independent of the essential NatA activity.
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Affiliation(s)
- Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Annika Brünje
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | | | - Thierry Meinnel
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Carmela Giglione
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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38
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Bader I, McTiernan N, Darbakk C, Boltshauser E, Ree R, Ebner S, Mayr JA, Arnesen T. Severe syndromic ID and skewed X-inactivation in a girl with NAA10 dysfunction and a novel heterozygous de novo NAA10 p.(His16Pro) variant - a case report. BMC MEDICAL GENETICS 2020; 21:153. [PMID: 32698785 PMCID: PMC7374887 DOI: 10.1186/s12881-020-01091-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/12/2020] [Indexed: 01/20/2023]
Abstract
BACKGROUND NAA10 is the catalytic subunit of the major N-terminal acetyltransferase complex NatA which acetylates almost half the human proteome. Over the past decade, many NAA10 missense variants have been reported as causative of genetic disease in humans. Individuals harboring NAA10 variants often display variable degrees of intellectual disability (ID), developmental delay, and cardiac anomalies. Initially, carrier females appeared to be oligo- or asymptomatic with X-inactivation pattern skewed towards the wild type allele. However, recently it has been shown that NAA10 variants can cause syndromic or non-syndromic intellectual disability in females as well. The impact of specific NAA10 variants and the X-inactivation pattern on the individual phenotype in females remains to be elucidated. CASE PRESENTATION Here we present a novel de novo NAA10 (NM_003491.3) c.[47A > C];[=] (p.[His16Pro];[=]) variant identified in a young female. The 10-year-old girl has severely delayed motor and language development, disturbed behavior with hyperactivity and restlessness, moderate dilatation of the ventricular system and extracerebral CSF spaces. Her blood leukocyte X-inactivation pattern was skewed (95/5) towards the maternally inherited X-chromosome. Our functional study indicates that NAA10 p.(H16P) impairs NatA complex formation and NatA catalytic activity, while monomeric NAA10 catalytic activity appears to be intact. Furthermore, cycloheximide experiments show that the NAA10 H16P variant does not affect the cellular stability of NAA10. DISCUSSION AND CONCLUSIONS We demonstrate that NAA10 p.(His16Pro) causes a severe form of syndromic ID in a girl most likely through impaired NatA-mediated Nt-acetylation of cellular proteins. X-inactivation analyses showed a skewed X-inactivation pattern in DNA from blood of the patient with the maternally inherited allele being preferentially methylated/inactivated.
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Affiliation(s)
- Ingrid Bader
- Einheit für Klinische Genetik, Universitätsklinik für Kinder- und Jugendheilkunde, Paracelsus Medizinische Universität, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sabine Ebner
- Einheit für Klinische Genetik, Universitätsklinik für Kinder- und Jugendheilkunde, Paracelsus Medizinische Universität, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Johannes A. Mayr
- Children’s Hospital, Paracelsus Medical University, Salzburg, Austria
| | - 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
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39
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Feng J, Hu J, Li Y, Li R, Yu H, Ma L. The N-Terminal Acetyltransferase Naa50 Regulates Arabidopsis Growth and Osmotic Stress Response. ACTA ACUST UNITED AC 2020; 61:1565-1575. [DOI: 10.1093/pcp/pcaa081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/08/2020] [Indexed: 11/14/2022]
Abstract
Abstract
N-terminal acetylation (Nt-acetylation) is one of the most common protein modifications in eukaryotes. The function of Naa50, the catalytic subunit of the evolutionarily conserved N-terminal acetyltransferase (Nat) E complex, has not been reported in Arabidopsis. In this study, we found that a loss of Naa50 resulted in a pleiotropic phenotype that included dwarfism and sterility, premature leaf senescence and a shortened primary root. Further analysis revealed that root cell patterning and various root cell properties were severely impaired in naa50 mutant plants. Moreover, defects in auxin distribution were observed due to the mislocalization of PIN auxin transporters. In contrast to its homologs in yeast and animals, Naa50 showed no co-immunoprecipitation with any subunit of the Nat A complex. Moreover, plants lacking Naa50 displayed hypersensitivity to abscisic acid and osmotic stress. Therefore, our results suggest that protein N-terminal acetylation catalyzed by Naa50 plays an essential role in Arabidopsis growth and osmotic stress responses.
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Affiliation(s)
- Jinlin Feng
- College of Life Sciences, Shanxi Normal University, Linfen, Shanxi 041004, China
| | - Jianxin Hu
- College of Life Sciences, Shanxi Normal University, Linfen, Shanxi 041004, China
| | - Yan Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ruiqi Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hao Yu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ligeng Ma
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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40
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The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb. Nat Commun 2020; 11:1504. [PMID: 32198371 PMCID: PMC7083937 DOI: 10.1038/s41467-020-15313-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
The conserved ribosome-associated complex (RAC) consisting of Zuo1 (Hsp40) and Ssz1 (non-canonical Hsp70) acts together with the ribosome-bound Hsp70 chaperone Ssb in de novo protein folding at the ribosomal tunnel exit. Current models suggest that the function of Ssz1 is confined to the support of Zuo1, however, it is not known whether RAC by itself serves as a chaperone for nascent chains. Here we show that, via its rudimentary substrate binding domain (SBD), Ssz1 directly binds to emerging nascent chains prior to Ssb. Structural and biochemical analyses identify a conserved LP-motif at the Zuo1 N-terminus forming a polyproline-II helix, which binds to the Ssz1-SBD as a pseudo-substrate. The LP-motif competes with nascent chain binding to the Ssz1-SBD and modulates nascent chain transfer. The combined data indicate that Ssz1 is an active chaperone optimized for transient, low-affinity substrate binding, which ensures the flux of nascent chains through RAC/Ssb. The ribosome-associated complex (RAC), which contains the Hsp40 protein Zuo1 and the non-canonical Hsp70 protein Ssz1 forms a chaperone triad with the fungal-specific Hsp70 protein Ssb. Here the authors combine X-ray crystallography, crosslinking and biochemical experiments and present the structure of the Zuo1 N-terminus bound to Ssz1 and demonstrate that Ssz1 is an active chaperone for nascent chains.
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41
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Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun 2020; 11:818. [PMID: 32042062 PMCID: PMC7010799 DOI: 10.1038/s41467-020-14584-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/18/2020] [Indexed: 01/04/2023] Open
Abstract
The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Lyon GJ. From Molecular Understanding to Organismal Biology of N-Terminal Acetyltransferases. Structure 2019; 27:1053-1055. [PMID: 31269458 DOI: 10.1016/j.str.2019.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this issue of Structure, Deng et al. (2019) determine the structure of the yeast N-terminal acetyltransferases Naa10 and Naa50 in complex with Naa15 and demonstrate that Naa50 has negligible catalytic activity on its own but modulates Naa10/Naa15. This study provides insights into mechanisms involving amino-terminal acetylation of proteins.
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Affiliation(s)
- Gholson J Lyon
- Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY 10314, USA; Biology PhD Program, The Graduate Center, The City University of New York, NY 10016, USA.
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Deng S, Magin RS, Wei X, Pan B, Petersson EJ, Marmorstein R. Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex. Structure 2019; 27:1057-1070.e4. [PMID: 31155310 PMCID: PMC6610660 DOI: 10.1016/j.str.2019.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 01/07/2023]
Abstract
NatA co-translationally acetylates the N termini of over 40% of eukaryotic proteins and can associate with another catalytic subunit, Naa50, to form a ternary NatA/Naa50 dual enzyme complex (also called NatE). The molecular basis of association between Naa50 and NatA and the mechanism for how their association affects their catalytic activities in yeast and human are poorly understood. Here, we determined the X-ray crystal structure of yeast NatA/Naa50 as a scaffold to understand coregulation of NatA/Naa50 activity in both yeast and human. We find that Naa50 makes evolutionarily conserved contacts to both the Naa10 and Naa15 subunits of NatA. These interactions promote catalytic crosstalk within the human complex, but do so to a lesser extent in the yeast complex, where Naa50 activity is compromised. These studies have implications for understanding the role of the NatA/Naa50 complex in modulating the majority of the N-terminal acetylome in diverse species.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert S Magin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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44
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Ree R, Geithus AS, Tørring PM, Sørensen KP, Damkjær M, Lynch SA, Arnesen T. A novel NAA10 p.(R83H) variant with impaired acetyltransferase activity identified in two boys with ID and microcephaly. BMC MEDICAL GENETICS 2019; 20:101. [PMID: 31174490 PMCID: PMC6554967 DOI: 10.1186/s12881-019-0803-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/08/2019] [Indexed: 12/21/2022]
Abstract
Background N-terminal acetylation is a common protein modification in human cells and is catalysed by N-terminal acetyltransferases (NATs), mostly cotranslationally. The NAA10-NAA15 (NatA) protein complex is the major NAT, responsible for acetylating ~ 40% of human proteins. Recently, NAA10 germline variants were found in patients with the X-linked lethal Ogden syndrome, and in other familial or de novo cases with variable degrees of developmental delay, intellectual disability (ID) and cardiac anomalies. Methods Here we report a novel NAA10 (NM_003491.3) c.248G > A, p.(R83H) missense variant in NAA10 which was detected by whole exome sequencing in two unrelated boys with intellectual disability, developmental delay, ADHD like behaviour, very limited speech and cardiac abnormalities. We employ in vitro acetylation assays to functionally test the impact of this variant on NAA10 enzyme activity. Results Functional characterization of NAA10-R83H by in vitro acetylation assays revealed a reduced enzymatic activity of monomeric NAA10-R83H. This variant is modelled to have an altered charge density in the acetyl-coenzyme A (Ac-CoA) binding region of NAA10. Conclusions We show that NAA10-R83H has a reduced monomeric catalytic activity, likely due to impaired enzyme-Ac-CoA binding. Our data support a model where reduced NAA10 and/or NatA activity cause the phenotypes observed in the two patients. Electronic supplementary material The online version of this article (10.1186/s12881-019-0803-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rasmus Ree
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5020, Bergen, Norway
| | - Anni Sofie Geithus
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5020, Bergen, Norway
| | | | | | - Mads Damkjær
- Hans Christian Andersen Children's Hospital, Odense University Hospital, DK-5000, Odense C, Denmark
| | | | - Sally Ann Lynch
- Temple Street Children's Hospital, Temple Street, Dublin, D01 X584, Ireland.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5020, Bergen, Norway. .,Department of Biological Sciences, University of Bergen, NO-5020, Bergen, Norway. .,Department of Surgery, Haukeland University Hospital, NO-5021, Bergen, Norway.
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45
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Fujii K, Susanto TT, Saurabh S, Barna M. Decoding the Function of Expansion Segments in Ribosomes. Mol Cell 2019; 72:1013-1020.e6. [PMID: 30576652 DOI: 10.1016/j.molcel.2018.11.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
Abstract
Expansion segments (ESs) are enigmatic insertions within the eukaryotic ribosome, the longest of which resemble tentacle-like extensions that vary in length and sequence across evolution, with a largely unknown function. By selectively engineering rRNA in yeast, we find that one of the largest ESs, ES27L, has an unexpected function in translation fidelity. Ribosomes harboring a deletion in the distal portion of ES27L have increased amino acid misincorporation, as well as readthrough and frameshifting errors. By employing quantitative mass spectrometry, we further find that ES27L acts as an RNA scaffold to facilitate binding of a conserved enzyme, methionine amino peptidase (MetAP). We show that MetAP unexpectedly controls the accuracy of ribosome decoding, which is coupled to an increase in its enzymatic function through its interaction with ES27L. These findings reveal that variable ESs of the ribosome serve important functional roles and act as platforms for the binding of proteins that modulate translation across evolution.
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Affiliation(s)
- Kotaro Fujii
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Teodorus Theo Susanto
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Saumya Saurabh
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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46
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Characterization of Evolutionarily Conserved Trypanosoma cruzi NatC and NatA-N-Terminal Acetyltransferase Complexes. J Parasitol Res 2019; 2019:6594212. [PMID: 30956813 PMCID: PMC6431383 DOI: 10.1155/2019/6594212] [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: 10/21/2018] [Revised: 01/16/2019] [Accepted: 02/03/2019] [Indexed: 11/29/2022] Open
Abstract
Protein N-terminal acetylation is a co- and posttranslational modification, conserved among eukaryotes. It determines the functional fate of many proteins including their stability, complex formation, and subcellular localization. N-terminal acetyltransferases (NATs) transfer an acetyl group to the N-termini of proteins, and the major NATs in yeast and humans are NatA, NatB, and NatC. In this study, we characterized the Trypanosoma cruzi (T. cruzi) NatC and NatA protein complexes, each consisting of one catalytic subunit and predicted auxiliary subunits. The proteins were found to be expressed in the three main life cycle stages of the parasite, formed stable complexes in vivo, and partially cosedimented with the ribosome in agreement with a cotranslational function. An in vitro acetylation assay clearly demonstrated that the acetylated substrates of the NatC catalytic subunit from T. cruzi were similar to those of yeast and human NatC, suggesting evolutionary conservation of function. An RNAi knockdown of the Trypanosoma brucei (T. brucei) NatC catalytic subunit indicated that reduced NatC-mediated N-terminal acetylation of target proteins reduces parasite growth.
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47
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Aksnes H, Ree R, Arnesen T. Co-translational, Post-translational, and Non-catalytic Roles of N-Terminal Acetyltransferases. Mol Cell 2019; 73:1097-1114. [PMID: 30878283 DOI: 10.1016/j.molcel.2019.02.007] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 02/07/2023]
Abstract
Recent studies of N-terminal acetylation have identified new N-terminal acetyltransferases (NATs) and expanded the known functions of these enzymes beyond their roles as ribosome-associated co-translational modifiers. For instance, the identification of Golgi- and chloroplast-associated NATs shows that acetylation of N termini also happens post-translationally. In addition, we now appreciate that some NATs are highly specific; for example, a dedicated NAT responsible for post-translational N-terminal acetylation of actin was recently revealed. Other studies have extended NAT function beyond Nt acetylation, including functions as lysine acetyltransferases (KATs) and non-catalytic roles. Finally, emerging studies emphasize the physiological relevance of N-terminal acetylation, including roles in calorie-restriction-induced longevity and pathological α-synuclein aggregation in Parkinson's disease. Combined, the NATs rise as multifunctional proteins, and N-terminal acetylation is gaining recognition as a major cellular regulator.
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Affiliation(s)
- Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Rasmus Ree
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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48
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Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome. Mol Cell 2019; 70:488-501.e5. [PMID: 29727619 DOI: 10.1016/j.molcel.2018.03.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/26/2018] [Accepted: 03/27/2018] [Indexed: 01/01/2023]
Abstract
Most eukaryotic proteins are N-terminally acetylated. This modification can be recognized as a signal for selective protein degradation (degron) by the N-end rule pathways. However, the prevalence and specificity of such degrons in the proteome are unclear. Here, by systematically examining how protein turnover is affected by N-terminal sequences, we perform a comprehensive survey of degrons in the yeast N-terminome. We find that approximately 26% of nascent protein N termini encode cryptic degrons. These degrons exhibit high hydrophobicity and are frequently recognized by the E3 ubiquitin ligase Doa10, suggesting a role in protein quality control. In contrast, N-terminal acetylation rarely functions as a degron. Surprisingly, we identify two pathways where N-terminal acetylation has the opposite function and blocks protein degradation through the E3 ubiquitin ligase Ubr1. Our analysis highlights the complexity of N-terminal degrons and argues that hydrophobicity, not N-terminal acetylation, is the predominant feature of N-terminal degrons in nascent proteins.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Florian Huber
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Robert A Knieß
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anna Bartosik
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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49
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Knorr AG, Schmidt C, Tesina P, Berninghausen O, Becker T, Beatrix B, Beckmann R. Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Nat Struct Mol Biol 2018; 26:35-39. [PMID: 30559462 DOI: 10.1038/s41594-018-0165-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
Abstract
The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation.
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Affiliation(s)
- Alexandra G Knorr
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Christian Schmidt
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Petr Tesina
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
| | - Birgitta Beatrix
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
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50
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Feng L, Jia H, Qin Y, Song Y, Tao S, Liu Y. Rapid Identification of Major QTL S Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae. Front Microbiol 2018; 9:2110. [PMID: 30254614 PMCID: PMC6141824 DOI: 10.3389/fmicb.2018.02110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022] Open
Abstract
Temperatures had a strong effect on many life history traits, including growth, development and reproduction. At near-freezing temperatures (0–4°C), yeast cells could trigger series of biochemical reactions to respond and adapt to the stress, protect them against sever cold and freeze injury. Different Saccharomyces cerevisiae strains vary greatly in their ability to grow at near-freezing temperatures. However, the molecular mechanisms that allow yeast cells to sustain this response are not yet fully understood and the genetic basis of tolerance and sensitivity to near-freeze stress remains unclear. Uncovering the genetic determinants of this trait is, therefore, of is of significant interest. In order to investigate the genetic basis that underlies near-freezing temperature tolerance in S. cerevisiae, we mapped the major quantitative trait loci (QTLs) using bulk segregant analysis (BSA) in the F2 segregant population of two Chinese indigenous S. cerevisiae strains with divergent tolerance capability at 4°C. By genome-wide comparison of single-nucleotide polymorphism (SNP) profiles between two bulks of segregants with high and low tolerance to near-freezing temperature, a hot region located on chromosome IV was identified tightly associated with the near-freezing temperature tolerance. The Reciprocal hemizygosity analysis (RHA) and gene deletion was used to validate the genes involved in the trait, showed that the gene NAT1 plays a role in the near-freezing temperature tolerance. This study improved our understanding of the genetic basis of the variability of near-freezing temperature tolerance in yeasts. The superior allele identified could be used to genetically improve the near-freezing stress adaptation of industrial yeast strains.
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Affiliation(s)
- Li Feng
- College of Enology, Northwest A&F University, Yangling, China
| | - He Jia
- College of Enology, Northwest A&F University, Yangling, China
| | - Yi Qin
- College of Enology, Northwest A&F University, Yangling, China
| | - Yuyang Song
- College of Enology, Northwest A&F University, Yangling, China
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, Yangling, China
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