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Jones BS, Pareek V, Hu DD, Weaver SD, Syska C, Galfano G, Champion MM, Champion PA. N - acetyl-transferases required for iron uptake and aminoglycoside resistance promote virulence lipid production in M. marinum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602253. [PMID: 39005365 PMCID: PMC11245092 DOI: 10.1101/2024.07.05.602253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Phagosomal lysis is a key aspect of mycobacterial infection of host macrophages. Acetylation is a protein modification mediated enzymatically by N-acetyltransferases (NATs) that impacts bacterial pathogenesis and physiology. To identify NATs required for lytic activity, we leveraged Mycobacterium marinum, a nontubercular pathogen and an established model for M. tuberculosis. M. marinum hemolysis is a proxy for phagolytic activity. We generated M. marinum strains with deletions in conserved NAT genes and screened for hemolytic activity. Several conserved lysine acetyltransferases (KATs) contributed to hemolysis. Hemolysis is mediated by the ESX-1 secretion system and by phthiocerol dimycocerosate (PDIM), a virulence lipid. For several strains, the hemolytic activity was restored by the addition of second copy of the ESX-1 locus. Using thin-layer chromatography (TLC), we found a single NAT required for PDIM and phenolic glycolipid (PGL) production. MbtK is a conserved KAT required for mycobactin siderophore synthesis and virulence. Mycobactin J exogenously complemented PDIM/PGL production in the Δ mbtK strain. The Δ mbtK M. marinum strain was attenuated in macrophage and Galleria mellonella infection models. Constitutive expression of either eis or papA5, which encode a KAT required for aminoglycoside resistance and a PDIM/PGL biosynthetic enzyme, rescued PDIM/PGL production and virulence of the Δ mbtK strain. Eis N-terminally acetylated PapA5 in vitro , supporting a mechanism for restored lipid production. Overall, our study establishes connections between the MbtK and Eis NATs, and between iron uptake and PDIM and PGL synthesis in M. marinum . Our findings underscore the multifunctional nature of mycobacterial NATs and their connection to key virulence pathways. Significance Statement Acetylation is a modification of protein N-termini, lysine residues, antibiotics and lipids. Many of the enzymes that promote acetylation belong to the GNAT family of proteins. M. marinum is a well-established as a model to understand how M. tuberculosis causes tuberculosis. In this study we sought to identify conserved GNAT proteins required for early stages of mycobacterial infection. Using M. marinum, we determined that several GNAT proteins are required for the lytic activity of M. marinum. We uncovered previously unknown connections between acetyl-transferases required for iron uptake and antimicrobial resistance, and the production of the unique mycobacterial lipids, PDIM and PGLOur data support that acetyl-transferases from the GNAT family are interconnected, and have activities beyond those previously reported.
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2
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Calis S, Gevaert K. The role of Nα-terminal acetylation in protein conformation. FEBS J 2024. [PMID: 38923676 DOI: 10.1111/febs.17209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Especially in higher eukaryotes, the N termini of proteins are subject to enzymatic modifications, with the acetylation of the alpha-amino group of nascent polypeptides being a prominent one. In recent years, the specificities and substrates of the enzymes responsible for this modification, the Nα-terminal acetyltransferases, have been mapped in several proteomic studies. Aberrant expression of, and mutations in these enzymes were found to be associated with several human diseases, explaining the growing interest in protein Nα-terminal acetylation. With some enzymes, such as the Nα-terminal acetyltransferase A complex having thousands of possible substrates, researchers are now trying to decipher the functional outcome of Nα-terminal protein acetylation. In this review, we zoom in on one possible functional consequence of Nα-terminal protein acetylation; its effect on protein folding. Using selected examples of proteins associated with human diseases such as alpha-synuclein and huntingtin, here, we discuss the sometimes contradictory findings of the effects of Nα-terminal protein acetylation on protein (mis)folding and aggregation.
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Affiliation(s)
- Sam Calis
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
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3
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Lyon GJ, Longo J, Garcia A, Inusa F, Marchi E, Shi D, Dörfel M, Arnesen T, Aldabe R, Lyons S, Nashat MA, Bolton D. Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. PLoS One 2024; 19:e0301328. [PMID: 38713657 PMCID: PMC11075865 DOI: 10.1371/journal.pone.0301328] [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: 07/20/2023] [Accepted: 03/14/2024] [Indexed: 05/09/2024] Open
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/y male mice on the inbred genetic background in this different animal facility.
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Affiliation(s)
- Gholson J. Lyon
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Joseph Longo
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Andrew Garcia
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Fatima Inusa
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Daniel Shi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Max Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - 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
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, CIMA, University of Navarra, Pamplona, Spain
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Melissa A. Nashat
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - David Bolton
- Molecular Biology Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
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4
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Daly RE, Myasnikov I, Gaglia MM. N-terminal acetylation separately promotes nuclear localization and host shutoff activity of the influenza A virus ribonuclease PA-X. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.01.569683. [PMID: 38076881 PMCID: PMC10705558 DOI: 10.1101/2023.12.01.569683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
To counteract host antiviral responses, influenza A virus triggers a global reduction of cellular gene expression, a process termed "host shutoff." A key effector of influenza A virus host shutoff is the viral endoribonuclease PA-X, which degrades host mRNAs. While many of the molecular determinants of PA-X activity remain unknown, a previous study found that N-terminal acetylation of PA-X is required for its host shutoff activity. However, it remains unclear how this co-translational modification promotes PA-X activity. Here, we report that PA-X N-terminal acetylation has two functions that can be separated based on the position of the acetylation, i.e. on the first amino acid, the initiator methionine, or the second amino acid following initiator methionine excision. Modification at either site is sufficient to ensure PA-X localization to the nucleus. However, modification of the second amino acid is not sufficient for host shutoff activity of ectopically expressed PA-X, which specifically requires N-terminal acetylation of the initiator methionine. Interestingly, during infection N-terminal acetylation of PA-X at any position results in host shutoff activity, which is in part due to a functional interaction with the influenza protein NS1. This result reveals an unexpected role for another viral protein in PA-X activity. Our studies uncover a multifaceted role for PA-X N-terminal acetylation in regulation of this important immunomodulatory factor.
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Affiliation(s)
- Raecliffe E Daly
- Program in Cellular, Molecular and Developmental Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA, 02111, United States
- Institute for Molecular Virology and Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI, 53706, United States
| | - Idalia Myasnikov
- Institute for Molecular Virology and Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI, 53706, United States
| | - Marta Maria Gaglia
- Institute for Molecular Virology and Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI, 53706, United States
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5
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Huang Z, Ito M, Zhang S, Toda T, Takeda JI, Ogi T, Ohno K. Extremely low-frequency electromagnetic field induces acetylation of heat shock proteins and enhances protein folding. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115482. [PMID: 37717354 DOI: 10.1016/j.ecoenv.2023.115482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/21/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
The pervasive weak electromagnetic fields (EMF) inundate the industrialized society, but the biological effects of EMF as weak as 10 µT have been scarcely analyzed. Heat shock proteins (HSPs) are molecular chaperones that mediate a sequential stress response. HSP70 and HSP90 provide cells under undesirable situations with either assisting covalent folding of proteins or degrading improperly folded proteins in an ATP-dependent manner. Here we examined the effect of extremely low-frequency (ELF)-EMF on AML12 and HEK293 cells. Although the protein expression levels of HSP70 and HSP90 were reduced after an exposure to ELF-EMF for 3 h, acetylations of HSP70 and HSP90 were increased, which was followed by an enhanced binding affinities of HSP70 and HSP90 for HSP70/HSP90-organizing protein (HOP/STIP1). After 3 h exposure to ELF-EMF, the amount of mitochondria was reduced but the ATP level and the maximal mitochondrial oxygen consumption were increased, which was followed by the reduced protein aggregates and the increased cell viability. Thus, ELF-EMF exposure for 3 h activated acetylation of HSPs to enhance protein folding, which was returned to the basal level at 12 h. The proteostatic effects of ELF-EMF will be able to be applied to treat pathological states in humans.
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Affiliation(s)
- Zhizhou Huang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shaochuan Zhang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takuro Toda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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6
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Zu G, Sun Z, Chen Y, Geng J, Lv J, You Z, Jiang C, Sheng Q, Nie Z. The acetyltransferase BmCBP changes the acetylation modification of BmSP3 and affects its protein expression in silkworm, Bombyx mori. Mol Biol Rep 2023; 50:8509-8521. [PMID: 37642757 DOI: 10.1007/s11033-023-08699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Protein acetylation is an important post-translational modification (PTM) that widely exists in organisms. As a reversible PTM, acetylation modification can regulate the function of proteins with high efficiency. In the previous study, the acetylation sites of silkworm proteins were identified on a large scale by nano-HPLC/MS/MS (nanoscale high performance liquid chromatography-tandem secondary mass spectrometry), and a total of 11 acetylation sites were discovered on Bombyx mori nutrient-storage protein SP3 (BmSP3). The purpose of this study was to investigate the effect of acetylation level on BmSP3. METHODS AND RESULTS In this study, the acetylation of BmSP3 was further verified by immunoprecipitation (IP) and Western blotting. Then, it was confirmed that acetylation could up-regulate the expression of BmSP3 by improving its protein stability in BmN cells. Co-IP and RNAi experiments showed acetyltransferase BmCBP could bind to BmSP3 and catalyze its acetylation modification, then regulate the expression of BmSP3. Furthermore, the knock-down of BmCBP could improve the ubiquitination level of BmSP3. Both acetylation and ubiquitination occur on the side chain of lysine residues, therefore, we speculated that the acetylation of BmSP3 catalyzed by BmCBP could competitively inhibit its ubiquitination modification and improve its protein stability by inhibiting ubiquitin-mediated proteasome degradation pathway, and thereby increase the expression and intracellular accumulation. CONCLUSIONS BmCBP catalyzes the acetylation of BmSP3 and may improve the stability of BmSP3 by competitive ubiquitination. This conclusion provides a new functional basis for the extensive involvement of acetylation in the regulation of nutrient storage and utilization in silkworm, Bombyx mori.
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Affiliation(s)
- Guowei Zu
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zihan Sun
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Yanmei Chen
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jiasheng Geng
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jiao Lv
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zhengying You
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Caiying Jiang
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Qing Sheng
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zuoming Nie
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
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7
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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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8
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Chen P, Huang R, Hazbun TR. Unlocking the Mysteries of Alpha-N-Terminal Methylation and its Diverse Regulatory Functions. J Biol Chem 2023:104843. [PMID: 37209820 PMCID: PMC10293735 DOI: 10.1016/j.jbc.2023.104843] [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: 08/17/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Protein post-translation modifications (PTMs) are a critical regulatory mechanism of protein function. Protein α-N-terminal (Nα) methylation is a conserved PTM across prokaryotes and eukaryotes. Studies of the Nα methyltransferases responsible for Να methylation and their substrate proteins have shown that the PTM involves diverse biological processes, including protein synthesis and degradation, cell division, DNA damage response, and transcription regulation. This review provides an overview of the progress toward the regulatory function of Να methyltransferases and their substrate landscape. More than 200 proteins in humans and 45 in yeast are potential substrates for protein Nα methylation based on the canonical recognition motif, XP[KR]. Based on recent evidence for a less stringent motif requirement, the number of substrates might be increased, but further validation is needed to solidify this concept. A comparison of the motif in substrate orthologs in selected eukaryotic species indicates intriguing gain and loss of the motif across the evolutionary landscape. We discuss the state of knowledge in the field that has provided insights into the regulation of protein Να methyltransferases and their role in cellular physiology and disease. We also outline the current research tools that are key to understanding Να methylation. Finally, challenges are identified and discussed that would aid in unlocking a system-level view of the roles of Να methylation in diverse cellular pathways.
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Affiliation(s)
- Panyue Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tony R Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.
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9
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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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10
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Significance of NatB-mediated N-terminal acetylation of auxin biosynthetic enzymes in maintaining auxin homeostasis in Arabidopsis thaliana. Commun Biol 2022; 5:1410. [PMID: 36550195 PMCID: PMC9780221 DOI: 10.1038/s42003-022-04313-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The auxin IAA (Indole-3-acetic acid) plays key roles in regulating plant growth and development, which depends on an intricate homeostasis that is determined by the balance between its biosynthesis, metabolism and transport. YUC flavin monooxygenases catalyze the rate-limiting step of auxin biosynthesis via IPyA (indole pyruvic acid) and are critical targets in regulating auxin homeostasis. Despite of numerous reports on the transcriptional regulation of YUC genes, little is known about those at the post-translational protein level. Here, we show that loss of function of CKRC3/TCU2, the auxiliary subunit (Naa25) of Arabidopsis NatB, and/or of its catalytic subunit (Naa20), NBC, led to auxin-deficiency in plants. Experimental evidences show that CKRC3/TCU2 can interact with NBC to form a NatB complex, catalyzing the N-terminal acetylation (NTA) of YUC proteins for their intracellular stability to maintain normal auxin homeostasis in plants. Hence, our findings provide significantly new insight into the link between protein NTA and auxin biosynthesis in plants.
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11
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Donnarumma F, Tucci V, Ambrosino C, Altucci L, Carafa V. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. Clin Epigenetics 2022; 14:182. [PMID: 36539894 PMCID: PMC9769039 DOI: 10.1186/s13148-022-01402-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Chromatin structural organization, gene expression and proteostasis are intricately regulated in a wide range of biological processes, both physiological and pathological. Protein acetylation, a major post-translational modification, is tightly involved in interconnected biological networks, modulating the activation of gene transcription and protein action in cells. A very large number of studies describe the pivotal role of the so-called acetylome (accounting for more than 80% of the human proteome) in orchestrating different pathways in response to stimuli and triggering severe diseases, including cancer. NAA60/NatF (N-terminal acetyltransferase F), also named HAT4 (histone acetyltransferase type B protein 4), is a newly discovered acetyltransferase in humans modifying N-termini of transmembrane proteins starting with M-K/M-A/M-V/M-M residues and is also thought to modify lysine residues of histone H4. Because of its enzymatic features and unusual cell localization on the Golgi membrane, NAA60 is an intriguing acetyltransferase that warrants biochemical and clinical investigation. Although it is still poorly studied, this review summarizes current findings concerning the structural hallmarks and biological role of this novel targetable epigenetic enzyme.
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Affiliation(s)
- Federica Donnarumma
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy
| | - Valeria Tucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Concetta Ambrosino
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.47422.370000 0001 0724 3038Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Lucia Altucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Vincenzo Carafa
- grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
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12
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Malinow RA, Zhu M, Jin Y, Kim KW. Forward genetic screening identifies novel roles for N-terminal acetyltransferase C and histone deacetylase in C. elegans development. Sci Rep 2022; 12:16438. [PMID: 36180459 PMCID: PMC9525577 DOI: 10.1038/s41598-022-20361-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/12/2022] [Indexed: 02/02/2023] Open
Abstract
Coordinating the balance between development and stress responses is critical for organismal survival. However, the cellular signaling controlling this mechanism is not well understood. In Caenorhabditis elegans, it has been hypothesized that a genetic network regulated by NIPI-3/Tibbles may control the balance between animal development and immune response. Using a nipi-3(0) lethality suppressor screen in C. elegans, we reveal a novel role for N-terminal acetyltransferase C complex natc-1/2/3 and histone deacetylase hda-4, in the control of animal development. These signaling proteins act, at least in part, through a PMK-1 p38 MAP kinase pathway (TIR-1-NSY-1-SEK-1-PMK-1), which plays a critical role in the innate immunity against infection. Additionally, using a transcriptional reporter of SEK-1, a signaling molecule within this p38 MAP kinase system that acts directly downstream of C/EBP bZip transcription factor CEBP-1, we find unexpected positive control of sek-1 transcription by SEK-1 along with several other p38 MAP kinase pathway components. Together, these data demonstrate a role for NIPI-3 regulators in animal development, operating, at least in part through a PMK-1 p38 MAPK pathway. Because the C. elegans p38 MAP kinase pathway is well known for its role in cellular stress responses, the novel biological components and mechanisms pertaining to development identified here may also contribute to the balance between stress response and development.
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Affiliation(s)
- Rose Aria Malinow
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ming Zhu
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Kyung Won Kim
- Department of Life Science, Hallym University, Chuncheon, 24252, South Korea.
- Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, South Korea.
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13
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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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14
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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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15
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Gong X, Huang Y, Liang Y, Yuan Y, Liu Y, Han T, Li S, Gao H, Lv B, Huang X, Linster E, Wang Y, Wirtz M, Wang Y. OsHYPK-mediated protein N-terminal acetylation coordinates plant development and abiotic stress responses in rice. MOLECULAR PLANT 2022; 15:740-754. [PMID: 35381198 DOI: 10.1016/j.molp.2022.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/08/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
N-terminal acetylation is one of the most common protein modifications in eukaryotes, and approximately 40% of human and plant proteomes are acetylated by ribosome-associated N-terminal acetyltransferase A (NatA) in a co-translational manner. However, the in vivo regulatory mechanism of NatA and the global impact of NatA-mediated N-terminal acetylation on protein fate remain unclear. Here, we identify Huntingtin Yeast partner K (HYPK), an evolutionarily conserved chaperone-like protein, as a positive regulator of NatA activity in rice. We found that loss of OsHYPK function leads to developmental defects in rice plant architecture but increased resistance to abiotic stresses, attributable to perturbation of the N-terminal acetylome and accelerated global protein turnover. Furthermore, we demonstrated that OsHYPK is also a substrate of NatA and that N-terminal acetylation of OsHYPK promotes its own degradation, probably through the Ac/N-degron pathway, which could be induced by abiotic stresses. Taken together, our findings suggest that the OsHYPK-NatA complex plays a critical role in coordinating plant development and stress responses by dynamically regulating NatA-mediated N-terminal acetylation and global protein turnover, which are essential for maintaining adaptive phenotypic plasticity in rice.
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Affiliation(s)
- Xiaodi Gong
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqian Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Liang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Yundong Yuan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Yuhao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Tongwen Han
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Shujia Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hengbin Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Bo Lv
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Yonghong Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agriculture University, Taian, Shandong 271018, China.
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16
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Feng J, Qin M, Yao L, Li Y, Han R, Ma L. The N-terminal acetyltransferase Naa50 regulates tapetum degradation and pollen development in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111180. [PMID: 35151444 DOI: 10.1016/j.plantsci.2022.111180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
The N-terminal acetylation of proteins is a key modification in eukaryotes. However, knowledge of the biological function of N-terminal acetylation modification of proteins in plants is limited. Naa50 is the catalytic subunit of the N-terminal acetyltransferase NatE complex. We previously demonstrated that the absence of Naa50 leads to sterility in Arabidopsis thaliana. In the present study, the lack of Naa50 resulted in collapsed and sterile pollen in Arabidopsis. Further experiments showed that the mutation in Naa50 accelerated programmed cell death in the tapetum. Expression pattern analysis revealed the specific expression of Naa50 in the tapetum cells of anthers at 9-11 stages during pollen development, when tapetal programmed cell death occurred. Reciprocal cross analyses indicated that male sterility in naa50 is caused by sporophytic effects. mRNA sequencing and quantitative PCR of the closed buds showed that the deletion of Naa50 resulted in the upregulation of the cysteine protease coding gene CEP1 and impaired the expression of several genes involved in pollen wall deposition and pollen mitotic division. The collective data suggest that Naa50 balances the degradation of tapetum cells during anther development and plays an important role in pollen development by affecting several pathways.
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Affiliation(s)
- Jinlin Feng
- College of Life Sciences, Shanxi Normal University, Taiyuan, 030000 Shanxi, China; Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan, 030000 Shanxi, China.
| | - Minghui Qin
- College of Life Sciences, Shanxi Normal University, Taiyuan, 030000 Shanxi, China; Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan, 030000 Shanxi, China
| | - Lixia Yao
- College of Life Sciences, Shanxi Normal University, Taiyuan, 030000 Shanxi, China; Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan, 030000 Shanxi, China
| | - Yan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Rong Han
- College of Life Sciences, Shanxi Normal University, Taiyuan, 030000 Shanxi, China; Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan, 030000 Shanxi, China
| | - Ligeng Ma
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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17
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Xu Y, Shi Z, Bao L. An expanding repertoire of protein acylations. Mol Cell Proteomics 2022; 21:100193. [PMID: 34999219 PMCID: PMC8933697 DOI: 10.1016/j.mcpro.2022.100193] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023] Open
Abstract
Protein post-translational modifications play key roles in multiple cellular processes by allowing rapid reprogramming of individual protein functions. Acylation, one of the most important post-translational modifications, is involved in different physiological activities including cell differentiation and energy metabolism. In recent years, the progression in technologies, especially the antibodies against acylation and the highly sensitive and effective mass spectrometry–based proteomics, as well as optimized functional studies, greatly deepen our understanding of protein acylation. In this review, we give a general overview of the 12 main protein acylations (formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, glutarylation, palmitoylation, myristoylation, benzoylation, crotonylation, and 2-hydroxyisobutyrylation), including their substrates (histones and nonhistone proteins), regulatory enzymes (writers, readers, and erasers), biological functions (transcriptional regulation, metabolic regulation, subcellular targeting, protein–membrane interactions, protein stability, and folding), and related diseases (cancer, diabetes, heart disease, neurodegenerative disease, and viral infection), to present a complete picture of protein acylations and highlight their functional significance in future research. Provide a general overview of the 12 main protein acylations. Acylation of viral proteins promotes viral integration and infection. Hyperacylation of histone has antitumous and neuroprotective effects. MS is widely used in the identification of acylation but has its challenges.
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Affiliation(s)
- Yuxuan Xu
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Zhenyu Shi
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Li Bao
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China.
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18
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Sun Z, Ma Y, Liu Y, Lv J, Wang D, You Z, Jiang C, Sheng Q, Nie Z. The Acetylation Modification of SP1 Regulates the Protein Stability in Silkworm. Appl Biochem Biotechnol 2021; 194:1621-1635. [PMID: 34826090 DOI: 10.1007/s12010-021-03757-9] [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: 05/29/2021] [Accepted: 11/08/2021] [Indexed: 12/01/2022]
Abstract
Acetylation is a highly conservative and reversible post-translational modification. Acetylation modification can regulate gene expression by altering protein function and is widely identified in an increasing number of species. Previously, the acetylated proteome of silkworm was identified by combining acetylated polypeptide enrichment with nano-HPLC/MS/MS; the identification revealed that the SP proteins (SPs) were high acetylated. In this study, the acetylation of SP1, one of the SPs, was further confirmed using immunoprecipitation (IP) and Western blotting. Then, we found the acetylation could upregulate SP1 protein expression by enhancing the protein stability. Further research found that the acetylation of SP1 protein can competitively inhibit its ubiquitination and thus improve the stability and cell accumulation of SP1 protein by inhibiting the ubiquitin-mediated proteasome degradation pathway. This result provides a basis for acetylation to regulate the nutrient storage and utilization of silkworm.
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Affiliation(s)
- Zihan Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yafei Ma
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yue Liu
- Zhejiang Economic & Trade Polytechnic, Hangzhou, 310018, China
| | - Jiao Lv
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dan Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zhengying You
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Caiying Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qing Sheng
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zuoming Nie
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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19
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N-alpha-acetylation of Huntingtin protein increases its propensity to aggregate. J Biol Chem 2021; 297:101363. [PMID: 34732320 PMCID: PMC8640455 DOI: 10.1016/j.jbc.2021.101363] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Huntington’s disease (HD) is a neurodegenerative disorder caused by a poly-CAG expansion in the first exon of the HTT gene, resulting in an extended poly-glutamine tract in the N-terminal domain of the Huntingtin (Htt) protein product. Proteolytic fragments of the poly-glutamine–containing N-terminal domain form intranuclear aggregates that are correlated with HD. Post-translational modification of Htt has been shown to alter its function and aggregation properties. However, the effect of N-terminal Htt acetylation has not yet been considered. Here, we developed a bacterial system to produce unmodified or N-terminally acetylated and aggregation-inducible Htt protein. We used this system together with biochemical, biophysical, and imaging studies to confirm that the Htt N-terminus is an in vitro substrate for the NatA N-terminal acetyltransferase and show that N-terminal acetylation promotes aggregation. These studies represent the first link between N-terminal acetylation and the promotion of a neurodegenerative disease and implicates NatA-mediated Htt acetylation as a new potential therapeutic target in HD.
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20
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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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21
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Chen P, Paschoal Sobreira TJ, Hall MC, Hazbun TR. Discovering the N-Terminal Methylome by Repurposing of Proteomic Datasets. J Proteome Res 2021; 20:4231-4247. [PMID: 34382793 DOI: 10.1021/acs.jproteome.1c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein α-N-methylation is an underexplored post-translational modification involving the covalent addition of methyl groups to the free α-amino group at protein N-termini. To systematically explore the extent of α-N-terminal methylation in yeast and humans, we reanalyzed publicly accessible proteomic datasets to identify N-terminal peptides contributing to the α-N-terminal methylome. This repurposing approach found evidence of α-N-methylation of established and novel protein substrates with canonical N-terminal motifs of established α-N-terminal methyltransferases, including human NTMT1/2 and yeast Tae1. NTMT1/2 are implicated in cancer and aging processes but have unclear and context-dependent roles. Moreover, α-N-methylation of noncanonical sequences was surprisingly prevalent, suggesting unappreciated and cryptic methylation events. Analysis of the amino acid frequencies of α-N-methylated peptides revealed a [S]1-[S/A/Q]2 pattern in yeast and [A/N/G]1-[A/S/V]2-[A/G]3 in humans, which differs from the canonical motif. We delineated the distribution of the two types of prevalent N-terminal modifications, acetylation and methylation, on amino acids at the first position. We tested three potentially methylated proteins and confirmed the α-N-terminal methylation of Hsp31 by additional proteomic analysis and immunoblotting. The other two proteins, Vma1 and Ssa3, were found to be predominantly acetylated, indicating that proteomic searching for α-N-terminal methylation requires careful consideration of mass spectra. This study demonstrates the feasibility of reprocessing proteomic data for global α-N-terminal methylome investigations.
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Affiliation(s)
- Panyue Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tony R Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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22
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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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23
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Deng S, Gottlieb L, Pan B, Supplee J, Wei X, Petersson EJ, Marmorstein R. Molecular mechanism of N-terminal acetylation by the ternary NatC complex. Structure 2021; 29:1094-1104.e4. [PMID: 34019809 DOI: 10.1016/j.str.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022]
Abstract
Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic subunit and two auxiliary subunits, Naa35 and Naa38; and substrate selectivity profile that overlaps with NatE. Here, we report the cryoelectron microscopy structure of S. pombe NatC with a NatE/C-type bisubstrate analog and inositol hexaphosphate (IP6), and associated biochemistry studies. We find that the presence of three subunits is a prerequisite for normal NatC acetylation activity in yeast and that IP6 binds tightly to NatC to stabilize the complex. We also describe the molecular basis for IP6-mediated NatC complex stabilization and the overlapping yet distinct substrate profiles of NatC and NatE.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah Gottlieb
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Buyan Pan
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julianna Supplee
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, 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
| | - 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, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry, 231 South 34(th) Street, 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, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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24
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Bock AS, Murthy AC, Tang WS, Jovic N, Shewmaker F, Mittal J, Fawzi NL. N-terminal acetylation modestly enhances phase separation and reduces aggregation of the low-complexity domain of RNA-binding protein fused in sarcoma. Protein Sci 2021; 30:1337-1349. [PMID: 33547841 DOI: 10.1002/pro.4029] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/22/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) assembles via liquid-liquid phase separation (LLPS) into functional RNA granules and aggregates in amyotrophic lateral sclerosis associated neuronal inclusions. Several studies have demonstrated that posttranslational modification (PTM) can significantly alter FUS phase separation and aggregation, particularly charge-altering phosphorylation of the nearly uncharged N-terminal low complexity domain of FUS (FUS LC). However, the occurrence and impact of N-terminal acetylation on FUS phase separation remains unexplored, even though N-terminal acetylation is the most common PTM in mammals and changes the charge at the N-terminus. First, we find that FUS is predominantly acetylated in two human cell types and stress conditions. Next, we show that recombinant FUS LC can be acetylated when co-expressed with the NatA complex in Escherichia coli. Using NMR spectroscopy, we find that N-terminal acetylated FUS LC (FUS LC Nt-Ac) does not notably alter monomeric FUS LC structure or motions. Despite no difference in structure, Nt-Ac-FUS LC phase separates more avidly than unmodified FUS LC. More importantly, N-terminal acetylation of FUS LC reduces aggregation. Our findings highlight the importance of N-terminal acetylation of proteins that undergo physiological LLPS and pathological aggregation.
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Affiliation(s)
- Anna S Bock
- Graduate Program in Biotechnology, Brown University, Providence, Rhode Island, USA
| | - Anastasia C Murthy
- Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Wai Shing Tang
- Graduate Program in Physics, Brown University, Providence, Rhode Island, USA
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Frank Shewmaker
- Department of Biochemistry, Uniformed Services University, Bethesda, Maryland, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Nicolas L Fawzi
- The Robert J and Nancy D Carney Institute for Brain Science & Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
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25
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Human NAA30 can rescue yeast mak3∆ mutant growth phenotypes. Biosci Rep 2021; 41:227865. [PMID: 33600573 PMCID: PMC7938456 DOI: 10.1042/bsr20202828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
N-terminal acetylation is an irreversible protein modification that primarily occurs co-translationally, and is catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). The NatC complex (NAA30–NAA35–NAA38) is a major NAT enzyme, which was first described in yeast and estimated to N-terminally acetylate ∼20% of the proteome. The activity of NatC is crucial for the correct functioning of its substrates, which include translocation to the Golgi apparatus, the inner nuclear membrane as well as proper mitochondrial function. We show in comparative viability and growth assays that yeast cells lacking MAK3/NAA30 grow poorly in non-fermentable carbon sources and other stress conditions. By using two different experimental approaches and two yeast strains, we show that liquid growth assays are the method of choice when analyzing subtle growth defects, keeping loss of information to a minimum. We further demonstrate that human NAA30 can functionally replace yeast MAK3/NAA30. However, this depends on the genetic background of the yeast strain. These findings indicate that the function of MAK3/NAA30 is evolutionarily conserved from yeast to human. Our yeast system provides a powerful approach to study potential human NAA30 variants using a high-throughput liquid growth assay with various stress conditions.
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26
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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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27
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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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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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Du Z, Regan J, Bartom E, Wu WS, Zhang L, Goncharoff DK, Li L. Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses. Sci Rep 2020; 10:21838. [PMID: 33318504 PMCID: PMC7736884 DOI: 10.1038/s41598-020-77993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
Transcriptional regulators are prevalent among identified prions in Saccharomyces cerevisiae, however, it is unclear how prions affect genome-wide transcription. We show here that the prion ([SWI+]) and mutant (swi1∆) forms of Swi1, a subunit of the SWI/SNF chromatin-remodeling complex, confer dramatically distinct transcriptomic profiles. In [SWI+] cells, genes encoding for 34 transcription factors (TFs) and 24 Swi1-interacting proteins can undergo transcriptional modifications. Several TFs show enhanced aggregation in [SWI+] cells. Further analyses suggest that such alterations are key factors in specifying the transcriptomic signatures of [SWI+] cells. Interestingly, swi1∆ and [SWI+] impose distinct and oftentimes opposite effects on cellular functions. Translation-associated activities, in particular, are significantly reduced in swi1∆ cells. Although both swi1∆ and [SWI+] cells are similarly sensitive to thermal, osmotic and drought stresses, harmful, neutral or beneficial effects were observed for a panel of tested chemical stressors. Further analyses suggest that the environmental stress response (ESR) is mechanistically different between swi1∆ and [SWI+] cells—stress-inducible ESR (iESR) are repressed by [SWI+] but unchanged by swi1∆ while stress-repressible ESR (rESR) are induced by [SWI+] but repressed by swi1∆. Our work thus demonstrates primarily gain-of-function outcomes through transcriptomic modifications by [SWI+] and highlights a prion-mediated regulation of transcription and phenotypes in yeast.
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Affiliation(s)
- Zhiqiang Du
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA.
| | - Jeniece Regan
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA
| | - Elizabeth Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Li Zhang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA.,Chinese Institute for Brain Research, Genomics Center and HPC Core, Beijing, 102206, China
| | | | - Liming Li
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60011, USA.
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31
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Klaips CL, Gropp MHM, Hipp MS, Hartl FU. Sis1 potentiates the stress response to protein aggregation and elevated temperature. Nat Commun 2020; 11:6271. [PMID: 33293525 PMCID: PMC7722728 DOI: 10.1038/s41467-020-20000-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cells adapt to conditions that compromise protein conformational stability by activating various stress response pathways, but the mechanisms used in sensing misfolded proteins remain unclear. Moreover, aggregates of disease proteins often fail to induce a productive stress response. Here, using a yeast model of polyQ protein aggregation, we identified Sis1, an essential Hsp40 co-chaperone of Hsp70, as a critical sensor of proteotoxic stress. At elevated levels, Sis1 prevented the formation of dense polyQ inclusions and directed soluble polyQ oligomers towards the formation of permeable condensates. Hsp70 accumulated in a liquid-like state within this polyQ meshwork, resulting in a potent activation of the HSF1 dependent stress response. Sis1, and the homologous DnaJB6 in mammalian cells, also regulated the magnitude of the cellular heat stress response, suggesting a general role in sensing protein misfolding. Sis1/DnaJB6 functions as a limiting regulator to enable a dynamic stress response and avoid hypersensitivity to environmental changes.
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Affiliation(s)
- Courtney L Klaips
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Michael H M Gropp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Mark S Hipp
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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32
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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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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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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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35
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Li Z, Dogra V, Lee KP, Li R, Li M, Li M, Kim C. N-Terminal Acetylation Stabilizes SIGMA FACTOR BINDING PROTEIN1 Involved in Salicylic Acid-Primed Cell Death. PLANT PHYSIOLOGY 2020; 183:358-370. [PMID: 32139475 PMCID: PMC7210619 DOI: 10.1104/pp.19.01417] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 05/14/2023]
Abstract
N-terminal (Nt) acetylation (NTA) is an ample and irreversible cotranslational protein modification catalyzed by ribosome-associated Nt-acetyltransferases. NTA on specific proteins can act as a degradation signal (called an Ac/N-degron) for proteolysis in yeast and mammals. However, in plants, the biological relevance of NTA remains largely unexplored. In this study, we reveal that Arabidopsis (Arabidopsis thaliana) SIGMA FACTOR-BINDING PROTEIN1 (SIB1), a transcription coregulator and a positive regulator of salicylic acid-primed cell death, undergoes an absolute NTA on the initiator Met; Nt-acetyltransferase B (NatB) partly contributes to this modification. While NTA results in destabilization of certain target proteins, our genetic and biochemical analyses revealed that plant NatB-involved NTA instead renders SIB1 more stable. Given that the ubiquitin/proteasome system stimulates SIB1 degradation, it seems that the NTA-conferred stability ensures the timely expression of SIB1-dependent genes, mostly related to immune responses. Taking our findings together, here we report a noncanonical NTA-driven protein stabilization in land plants.
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Affiliation(s)
- Zihao Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Keun Pyo Lee
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rongxia Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingyue Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mengping Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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36
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Beigl TB, Hellesvik M, Saraste J, Arnesen T, Aksnes H. N-terminal acetylation of actin by NAA80 is essential for structural integrity of the Golgi apparatus. Exp Cell Res 2020; 390:111961. [PMID: 32209306 DOI: 10.1016/j.yexcr.2020.111961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 01/07/2023]
Abstract
N-alpha-acetyltransferase 80 (NAA80) was recently demonstrated to acetylate the N-terminus of actin, with NAA80 knockout cells showing actin cytoskeleton-related phenotypes, such as increased formation of membrane protrusions and accelerated migration. Here we report that NAA80 knockout cells additionally display fragmentation of the Golgi apparatus. We further employed rescue assays to demonstrate that this phenotype is connected to the ability of NAA80 to modify actin. Thus, re-expression of NAA80, which leads to re-establishment of actin's N-terminal acetyl group, rescued the Golgi fragmentation, whereas a catalytic dead NAA80 mutant could neither restore actin Nt-acetylation nor Golgi structure. The Golgi phenotype of NAA80 KO cells was shared by both migrating and non-migrating cells and live-cell imaging indicated increased Golgi dynamics in migrating NAA80 KO cells. Finally, we detected a drastic increase in the amount of F-actin in cells lacking NAA80, suggesting a causal relationship between this effect and the observed re-organization of Golgi structure. The findings further underscore the importance of actin Nt-acetylation and provide novel insight into its cellular roles, suggesting a mechanistic link between actin modification state and Golgi organization.
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Affiliation(s)
- Tobias B Beigl
- Department of Biomedicine, University of Bergen, Norway; Institute of Cell Biology and Immunology, University of Stuttgart, Germany
| | | | | | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Norway; Department of Biological Sciences, University of Bergen, Norway; Department of Surgery, Haukeland University Hospital, Norway
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37
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Schreiber KJ, Lewis JD. Protein Acetylation in Pathogen Virulence and Host Defense: In Vitro Detection of Protein Acetylation by Radiolabeled Acetyl Coenzyme A. Methods Mol Biol 2020; 1991:23-32. [PMID: 31041759 DOI: 10.1007/978-1-4939-9458-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein acetylation has emerged as a common modification that modulates multiple aspects of protein function, including localization, stability, and protein-protein interactions. It is increasingly evident that protein acetylation significantly impacts the outcome of host-microbe interactions. In order to characterize novel putative acetyltransferase enzymes and their substrates, we describe a simple protocol for the detection of acetyltransferase activity in vitro. Purified proteins are incubated with 14C-acetyl CoA and separated electrophoretically, and acetylated proteins are detected by phosphorimaging or autoradiography.
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Affiliation(s)
- Karl J Schreiber
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA. .,Plant Gene Expression Center, United States Department of Agriculture, Albany, CA, USA.
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38
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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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Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. Int J Mol Sci 2020; 21:ijms21030990. [PMID: 32024292 PMCID: PMC7037952 DOI: 10.3390/ijms21030990] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.
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40
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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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41
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Griffith AA, Holmes W. Fine Tuning: Effects of Post-Translational Modification on Hsp70 Chaperones. Int J Mol Sci 2019; 20:ijms20174207. [PMID: 31466231 PMCID: PMC6747426 DOI: 10.3390/ijms20174207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023] Open
Abstract
The discovery of heat shock proteins shaped our view of protein folding in the cell. Since their initial discovery, chaperone proteins were identified in all domains of life, demonstrating their vital and conserved functional roles in protein homeostasis. Chaperone proteins maintain proper protein folding in the cell by utilizing a variety of distinct, characteristic mechanisms to prevent aberrant intermolecular interactions, prevent protein aggregation, and lower entropic costs to allow for protein refolding. Continued study has found that chaperones may exhibit alternative functions, including maintaining protein folding during endoplasmic reticulum (ER) import and chaperone-mediated degradation, among others. Alternative chaperone functions are frequently controlled by post-translational modification, in which a given chaperone can switch between functions through covalent modification. This review will focus on the Hsp70 class chaperones and their Hsp40 co-chaperones, specifically highlighting the importance of post-translational control of chaperones. These modifications may serve as a target for therapeutic intervention in the treatment of diseases of protein misfolding and aggregation.
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Affiliation(s)
| | - William Holmes
- Rhode Island College, Biology Department, Providence, RI 02908, USA.
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42
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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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43
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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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Serio TR. [PIN+]ing down the mechanism of prion appearance. FEMS Yeast Res 2019; 18:4923032. [PMID: 29718197 PMCID: PMC5889010 DOI: 10.1093/femsyr/foy026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/03/2018] [Indexed: 11/13/2022] Open
Abstract
Prions are conformationally flexible proteins capable of adopting a native state and a spectrum of alternative states associated with a change in the function of the protein. These alternative states are prone to assemble into amyloid aggregates, which provide a structure for self-replication and transmission of the underlying conformer and thereby the emergence of a new phenotype. Amyloid appearance is a rare event in vivo, regulated by both the aggregation propensity of prion proteins and their cellular environment. How these forces normally intersect to suppress amyloid appearance and the ways in which these restrictions can be bypassed to create protein-only phenotypes remain poorly understood. The most widely studied and perhaps most experimentally tractable system to explore the mechanisms regulating amyloid appearance is the [PIN+] prion of Saccharomyces cerevisiae. [PIN+] is required for the appearance of the amyloid state for both native yeast proteins and for human proteins expressed in yeast. These observations suggest that [PIN+] facilitates the bypass of amyloid regulatory mechanisms by other proteins in vivo. Several models of prion appearance are compatible with current observations, highlighting the complexity of the process and the questions that must be resolved to gain greater insight into the mechanisms regulating these events.
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Affiliation(s)
- Tricia R Serio
- The University of Massachusetts-Amherst, Department of Biochemistry and Molecular Biology, 240 Thatcher Rd, N360, Amherst, MA 01003, USA
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45
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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: 155] [Impact Index Per Article: 31.0] [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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Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T. N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae. Mol Cell Proteomics 2018; 17:2309-2323. [PMID: 30150368 PMCID: PMC6283290 DOI: 10.1074/mcp.ra118.000982] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/22/2018] [Indexed: 12/17/2022] Open
Abstract
Nt-acetylation is a prevalent protein modification catalyzed by N-terminal acetyltransferases using acetyl-CoA as acetyl donor. Here, we performed a global analysis of Nt-acetylation in yeast following nutrient starvation. Contrary to histone acetylation, which is sensitive to acetyl-CoA levels, we demonstrate that Nt-acetylation remains largely unaffected to changes in cellular metabolism. We did, however, identify two protein groups that were differentially Nt-acetylated, one showing the same sensitivity to acetyl-CoA as histones. We propose that specific, rather than global, Nt-acetylation events are subject to metabolic regulation. N-terminal acetylation (Nt-acetylation) is a highly abundant protein modification in eukaryotes and impacts a wide range of cellular processes, including protein quality control and stress tolerance. Despite its prevalence, the mechanisms regulating Nt-acetylation are still nebulous. Here, we present the first global study of Nt-acetylation in yeast cells as they progress to stationary phase in response to nutrient starvation. Surprisingly, we found that yeast cells maintain their global Nt-acetylation levels upon nutrient depletion, despite a marked decrease in acetyl-CoA levels. We further observed two distinct sets of protein N termini that display differential and opposing Nt-acetylation behavior upon nutrient starvation, indicating a dynamic process. The first protein cluster was enriched for annotated N termini showing increased Nt-acetylation in stationary phase compared with exponential growth phase. The second protein cluster was conversely enriched for alternative nonannotated N termini (i.e. N termini indicative of shorter N-terminal proteoforms) and, like histones, showed reduced acetylation levels in stationary phase when acetyl-CoA levels were low. Notably, the degree of Nt-acetylation of Pcl8, a negative regulator of glycogen biosynthesis and two components of the pre-ribosome complex (Rsa3 and Rpl7a) increased during starvation. Moreover, the steady-state levels of these proteins were regulated both by starvation and NatA activity. In summary, this study represents the first comprehensive analysis of metabolic regulation of Nt-acetylation and reveals that specific, rather than global, Nt-acetylation events are subject to metabolic regulation.
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Affiliation(s)
- Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; Donnelly Center for Cellular and Bio‡molecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Fedor Kryuchkov
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium; VIB Proteomics Core, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium; VIB Proteomics Core, B-9000 Ghent, Belgium
| | - Veronique Jonckheere
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
| | - 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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Arnesen T, Marmorstein R, Dominguez R. Actin's N-terminal acetyltransferase uncovered. Cytoskeleton (Hoboken) 2018; 75:318-322. [PMID: 30084538 DOI: 10.1002/cm.21455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
Abstract
Humans express six highly conserved actin isoforms, which differ the most at their N-termini. Actin's N-terminus undergoes co- and post-translational processing unique among eukaryotic proteins. During translation, the initiator methionine of the two cytoplasmic isoforms is N-terminally acetylated (Nt-acetylated) and that of the four muscle isoforms is removed and the exposed cysteine is Nt-acetylated. Then, an unidentified acetylaminopeptidase post-translationally removes the Ac-Met (or Ac-Cys), and all six isoforms are re-acetylated at the N-terminus. Despite the vital importance of actin for cellular processes ranging from cell motility to organelle trafficking and cell division, the mechanism and functional consequences of Nt-acetylation remained unresolved. Two recent studies significantly advance our understanding of actin Nt-acetylation. Drazic et al. (2018, Proc Natl Acad Sci U S A, 115, 4399-4404) identify actin's dedicated N-terminal acetyltransferase (NAA80/NatH), and demonstrate that Nt-acetylation critically impacts actin assembly in vitro and in cells. NAA80 knockout cells display increased filopodia and lamellipodia formation and accelerated cell motility. In vitro, the absence of Nt-acetylation leads to a decrease in the rates of filament depolymerization and elongation, including formin-induced elongation. Goris et al. (2018, Proc Natl Acad Sci U S A, 115, 4405-4410] describe the structure of Drosophila NAA80 in complex with a peptide-CoA bi-substrate analog mimicking the N-terminus of β-actin. The structure reveals the source of NAA80's specificity for actin's negatively-charged N-terminus. Nt-acetylation neutralizes a positive charge, thus enhancing the overall negative charge of actin's unique N-terminus. Actin's N-terminus is exposed in the filament and influences the interactions of many actin-binding proteins. These advances open the way to understanding the many likely consequences and functional roles of actin Nt-acetylation.
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Affiliation(s)
- 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 Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Abstract
NAA10-related syndrome is an X-linked condition with a broad spectrum of findings ranging from a severe phenotype in males with p.Ser37Pro in NAA10, originally described as Ogden syndrome, to the milder NAA10-related intellectual disability found with different variants in both males and females. Although developmental impairments/intellectual disability may be the presenting feature (and in some cases the only finding), many individuals have additional cardiovascular, growth, and dysmorphic findings that vary in type and severity. Therefore, this set of disorders has substantial phenotypic variability and, as such, should be referred to more broadly as NAA10-related syndrome. NAA10 encodes an enzyme NAA10 that is certainly involved in the amino-terminal acetylation of proteins, alongside other proposed functions for this same protein. The mechanistic basis for how variants in NAA10 lead to the various phenotypes in humans is an active area of investigation, some of which will be reviewed herein. A detailed overview of a rare X-linked hereditary disorder gives clinicians a resource for making an informed diagnosis based on genetic data and developmental abnormalities. Around 80% of all human proteins are modified on their amino terminus via tagging with an acetyl group, and the NAA10 enzyme plays a major role in this process. Mutations in the gene encoding NAA10 produce severe neurological and cardiovascular effects. Yiyang Wu and Gholson Lyon at the Cold Spring Harbor Laboratory, Woodbury, USA, have reviewed current research to facilitate accurate identification of ‘NAA10-related syndrome’. Since this gene resides on the X chromosome, mutations strongly affect males, although some female carriers also show symptoms. NAA10-related syndrome is exceedingly rare, with only 26 cases reported to date, and the researchers describe both known causative mutations and unrelated disorders that produce similar developmental defects.
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Nguyen KT, Mun SH, Lee CS, Hwang CS. Control of protein degradation by N-terminal acetylation and the N-end rule pathway. Exp Mol Med 2018; 50:1-8. [PMID: 30054456 PMCID: PMC6063864 DOI: 10.1038/s12276-018-0097-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 11/10/2022] Open
Abstract
Nα-terminal acetylation (Nt-acetylation) occurs very frequently and is found in most proteins in eukaryotes. Despite the pervasiveness and universality of Nt-acetylation, its general functions in terms of physiological outcomes remain largely elusive. However, several recent studies have revealed that Nt-acetylation has a significant impact on protein stability, activity, folding patterns, cellular localization, etc. In addition, Nt-acetylation marks specific proteins for degradation by a branch of the N-end rule pathway, a subset of the ubiquitin-mediated proteolytic system. The N-end rule associates a protein's in vivo half-life with its N-terminal residue or modifications on its N-terminus. This review provides a current understanding of intracellular proteolysis control by Nt-acetylation and the N-end rule pathway.
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Affiliation(s)
- Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sang-Hyeon Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.
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Ree R, Varland S, Arnesen T. Spotlight on protein N-terminal acetylation. Exp Mol Med 2018; 50:1-13. [PMID: 30054468 PMCID: PMC6063853 DOI: 10.1038/s12276-018-0116-z] [Citation(s) in RCA: 261] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 01/11/2023] Open
Abstract
N-terminal acetylation (Nt-acetylation) is a widespread protein modification among eukaryotes and prokaryotes alike. By appending an acetyl group to the N-terminal amino group, the charge, hydrophobicity, and size of the N-terminus is altered in an irreversible manner. This alteration has implications for the lifespan, folding characteristics and binding properties of the acetylated protein. The enzymatic machinery responsible for Nt-acetylation has been largely described, but significant knowledge gaps remain. In this review, we provide an overview of eukaryotic N-terminal acetyltransferases (NATs) and the impact of Nt-acetylation. We also discuss other functions of known NATs and outline methods for studying Nt-acetylation.
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Affiliation(s)
- Rasmus Ree
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Sylvia Varland
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway
- Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway.
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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