1
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Larsen SK, Bekkelund ÅK, Glomnes N, Arnesen T, Aksnes H. Assessing N-terminal acetylation status of cellular proteins via an antibody specific for acetylated methionine. Biochimie 2024:S0300-9084(24)00166-4. [PMID: 39038730 DOI: 10.1016/j.biochi.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/01/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
N-terminal acetylation is being recognized as a factor affecting protein lifetime and proteostasis. It is a modification where an acetyl group is added to the N-terminus of proteins, and this occurs in 80 % of the human proteome. N-terminal acetylation is catalyzed by enzymes called N-terminal acetyltransferases (NATs). The various NATs acetylate different N-terminal amino acids, and methionine is a known target for some of the NATs. Currently, the acetylation status of most proteins can only be assessed with a limited number of methods, including mass spectrometry, which although powerful and robust, remains laborious and can only survey a fraction of the proteome. We here present testing of an antibody that was developed to specifically recognize Nt-acetylated methionine-starting proteins. We have used dot blots with synthetic acetylated and non-acetylated peptides in addition to protein analysis of lysates from NAT knockout cell lines to assess the specificity and application of this anti-Nt-acetylated methionine antibody (anti-NtAc-Met). Our results demonstrate that this antibody is indeed NtAc-specific and further show that it has selectivity for some subtypes of methionine-starting N-termini, specifically potential substrates of the NatC, NatE and NatF enzymes. We propose that this antibody may be a powerful tool to identify NAT substrates or to analyse changes in N-terminal acetylation for specific cellular proteins of interest.
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Affiliation(s)
| | - Åse K Bekkelund
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, 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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2
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Varland S, Silva RD, Kjosås I, Faustino A, Bogaert A, Billmann M, Boukhatmi H, Kellen B, Costanzo M, Drazic A, Osberg C, Chan K, Zhang X, Tong AHY, Andreazza S, Lee JJ, Nedyalkova L, Ušaj M, Whitworth AJ, Andrews BJ, Moffat J, Myers CL, Gevaert K, Boone C, Martinho RG, Arnesen T. N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity. Nat Commun 2023; 14:6774. [PMID: 37891180 PMCID: PMC10611716 DOI: 10.1038/s41467-023-42342-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Most eukaryotic proteins are N-terminally acetylated, but the functional impact on a global scale has remained obscure. Using genome-wide CRISPR knockout screens in human cells, we reveal a strong genetic dependency between a major N-terminal acetyltransferase and specific ubiquitin ligases. Biochemical analyses uncover that both the ubiquitin ligase complex UBR4-KCMF1 and the acetyltransferase NatC recognize proteins bearing an unacetylated N-terminal methionine followed by a hydrophobic residue. NatC KO-induced protein degradation and phenotypes are reversed by UBR knockdown, demonstrating the central cellular role of this interplay. We reveal that loss of Drosophila NatC is associated with male sterility, reduced longevity, and age-dependent loss of motility due to developmental muscle defects. Remarkably, muscle-specific overexpression of UbcE2M, one of the proteins targeted for NatC KO-mediated degradation, suppresses defects of NatC deletion. In conclusion, NatC-mediated N-terminal acetylation acts as a protective mechanism against protein degradation, which is relevant for increased longevity and motility.
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Affiliation(s)
- Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, N-5006, Bergen, Norway.
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Rui Duarte Silva
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal.
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139, Faro, Portugal.
| | - Ine Kjosås
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway
| | - Alexandra Faustino
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Annelies Bogaert
- VIB-UGent Center for Medical Biotechnology, B-9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, D-53127, Bonn, Germany
| | - Hadi Boukhatmi
- Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1, CNRS, UMR6290, 35065, Rennes, France
| | - Barbara Kellen
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Michael Costanzo
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway
| | - Camilla Osberg
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway
| | - Katherine Chan
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Xiang Zhang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Amy Hin Yan Tong
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Simonetta Andreazza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Juliette J Lee
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Lyudmila Nedyalkova
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Matej Ušaj
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | - Brenda J Andrews
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Jason Moffat
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, B-9052, Ghent, Belgium
| | - Charles Boone
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
- RIKEN Centre for Sustainable Resource Science, Wako, Saitama, 351-0106, Japan
| | - Rui Gonçalo Martinho
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139, Faro, Portugal.
- Departmento de Ciências Médicas, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
- iBiMED - Institute of Biomedicine, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5021, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, N-5006, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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3
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Varland S, Brønstad KM, Skinner SJ, Arnesen T. A nonsense variant in the N-terminal acetyltransferase NAA30 may be associated with global developmental delay and tracheal cleft. Am J Med Genet A 2023; 191:2402-2410. [PMID: 37387332 DOI: 10.1002/ajmg.a.63338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/03/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Most human proteins are N-terminally acetylated by N-terminal acetyltransferases (NATs), which play crucial roles in many cellular functions. The NatC complex, comprising the catalytic subunit NAA30 and the auxiliary subunits NAA35 and NAA38, is estimated to acetylate up to 20% of the human proteome in a co-translational manner. Several NAT enzymes have been linked to rare genetic diseases, causing developmental delay, intellectual disability, and heart disease. Here, we report a de novo heterozygous NAA30 nonsense variant c.244C>T (p.Q82*) (NM_001011713.2), which was identified by whole exome sequencing in a 5-year-old boy presenting with global development delay, autism spectrum disorder, hypotonia, tracheal cleft, and recurrent respiratory infections. Biochemical studies were performed to assess the functional impact of the premature stop codon on NAA30's catalytic activity. We find that NAA30-Q82* completely disrupts the N-terminal acetyltransferase activity toward a classical NatC substrate using an in vitro acetylation assay. This finding corresponds with structural modeling showing that the truncated NAA30 variant lacks the entire GNAT domain, which is required for catalytic activity. This study suggests that defective NatC-mediated N-terminal acetylation can cause disease, thus expanding the spectrum of NAT variants linked to genetic disease.
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Affiliation(s)
- Sylvia Varland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | | | - Stephanie J Skinner
- Department of Pediatrics, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
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4
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Biochemical analysis of novel NAA10 variants suggests distinct pathogenic mechanisms involving impaired protein N-terminal acetylation. Hum Genet 2022; 141:1355-1369. [PMID: 35039925 PMCID: PMC9304055 DOI: 10.1007/s00439-021-02427-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023]
Abstract
NAA10 is the catalytic subunit of the N-terminal acetyltransferase complex, NatA, which is responsible for N-terminal acetylation of nearly half the human proteome. Since 2011, at least 21 different NAA10 missense variants have been reported as pathogenic in humans. The clinical features associated with this X-linked condition vary, but commonly described features include developmental delay, intellectual disability, cardiac anomalies, brain abnormalities, facial dysmorphism and/or visual impairment. Here, we present eight individuals from five families with five different de novo or inherited NAA10 variants. In order to determine their pathogenicity, we have performed biochemical characterisation of the four novel variants c.16G>C p.(A6P), c.235C>T p.(R79C), c.386A>C p.(Q129P) and c.469G>A p.(E157K). Additionally, we clinically describe one new case with a previously identified pathogenic variant, c.384T>G p.(F128L). Our study provides important insight into how different NAA10 missense variants impact distinct biochemical functions of NAA10 involving the ability of NAA10 to perform N-terminal acetylation. These investigations may partially explain the phenotypic variability in affected individuals and emphasise the complexity of the cellular pathways downstream of NAA10.
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5
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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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6
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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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7
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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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Bader I, McTiernan N, Darbakk C, Boltshauser E, Ree R, Ebner S, Mayr JA, Arnesen T. Severe syndromic ID and skewed X-inactivation in a girl with NAA10 dysfunction and a novel heterozygous de novo NAA10 p.(His16Pro) variant - a case report. BMC MEDICAL GENETICS 2020; 21:153. [PMID: 32698785 PMCID: PMC7374887 DOI: 10.1186/s12881-020-01091-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/12/2020] [Indexed: 01/20/2023]
Abstract
BACKGROUND NAA10 is the catalytic subunit of the major N-terminal acetyltransferase complex NatA which acetylates almost half the human proteome. Over the past decade, many NAA10 missense variants have been reported as causative of genetic disease in humans. Individuals harboring NAA10 variants often display variable degrees of intellectual disability (ID), developmental delay, and cardiac anomalies. Initially, carrier females appeared to be oligo- or asymptomatic with X-inactivation pattern skewed towards the wild type allele. However, recently it has been shown that NAA10 variants can cause syndromic or non-syndromic intellectual disability in females as well. The impact of specific NAA10 variants and the X-inactivation pattern on the individual phenotype in females remains to be elucidated. CASE PRESENTATION Here we present a novel de novo NAA10 (NM_003491.3) c.[47A > C];[=] (p.[His16Pro];[=]) variant identified in a young female. The 10-year-old girl has severely delayed motor and language development, disturbed behavior with hyperactivity and restlessness, moderate dilatation of the ventricular system and extracerebral CSF spaces. Her blood leukocyte X-inactivation pattern was skewed (95/5) towards the maternally inherited X-chromosome. Our functional study indicates that NAA10 p.(H16P) impairs NatA complex formation and NatA catalytic activity, while monomeric NAA10 catalytic activity appears to be intact. Furthermore, cycloheximide experiments show that the NAA10 H16P variant does not affect the cellular stability of NAA10. DISCUSSION AND CONCLUSIONS We demonstrate that NAA10 p.(His16Pro) causes a severe form of syndromic ID in a girl most likely through impaired NatA-mediated Nt-acetylation of cellular proteins. X-inactivation analyses showed a skewed X-inactivation pattern in DNA from blood of the patient with the maternally inherited allele being preferentially methylated/inactivated.
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Affiliation(s)
- Ingrid Bader
- Einheit für Klinische Genetik, Universitätsklinik für Kinder- und Jugendheilkunde, Paracelsus Medizinische Universität, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sabine Ebner
- Einheit für Klinische Genetik, Universitätsklinik für Kinder- und Jugendheilkunde, Paracelsus Medizinische Universität, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Johannes A. Mayr
- Children’s Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
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9
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Rebowski G, Boczkowska M, Drazic A, Ree R, Goris M, Arnesen T, Dominguez R. Mechanism of actin N-terminal acetylation. SCIENCE ADVANCES 2020; 6:eaay8793. [PMID: 32284999 PMCID: PMC7141826 DOI: 10.1126/sciadv.aay8793] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/14/2020] [Indexed: 06/11/2023]
Abstract
About 80% of human proteins are amino-terminally acetylated (Nt-acetylated) by one of seven Nt-acetyltransferases (NATs). Actin, the most abundant protein in the cytoplasm, has its own dedicated NAT, NAA80, which acts posttranslationally and affects cytoskeleton assembly and cell motility. Here, we show that NAA80 does not associate with filamentous actin in cells, and its natural substrate is the monomeric actin-profilin complex, consistent with Nt-acetylation preceding polymerization. NAA80 Nt-acetylates actin-profilin much more efficiently than actin alone, suggesting that profilin acts as a chaperone for actin Nt-acetylation. We determined crystal structures of the NAA80-actin-profilin ternary complex, representing different actin isoforms and different states of the catalytic reaction and revealing the first structure of NAT-substrate complex at atomic resolution. The structural, biochemical, and cellular analysis of mutants shows how NAA80 has evolved to specifically recognize actin among all cellular proteins while targeting all six actin isoforms, which differ the most at the amino terminus.
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Affiliation(s)
- Grzegorz Rebowski
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Malgorzata Boczkowska
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Marianne Goris
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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10
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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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11
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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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A novel NAA10 variant with impaired acetyltransferase activity causes developmental delay, intellectual disability, and hypertrophic cardiomyopathy. Eur J Hum Genet 2018; 26:1294-1305. [PMID: 29748569 DOI: 10.1038/s41431-018-0136-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 11/09/2022] Open
Abstract
The NAA10-NAA15 complex (NatA) is an N-terminal acetyltransferase that catalyzes N-terminal acetylation of ~40% of all human proteins. N-terminal acetylation has several different roles in the cell, including altering protein stability and degradation, protein localization and protein-protein interactions. In recent years several X-linked NAA10 variants have been associated with genetic disorders. We have identified a previously undescribed NAA10 c.215T>C p.(Ile72Thr) variant in three boys from two unrelated families with a milder phenotypic spectrum in comparison to most of the previously described patients with NAA10 variants. These boys have development delay, intellectual disability, and cardiac abnormalities as overlapping phenotypes. Functional studies reveal that NAA10 Ile72Thr is destabilized, while binding to NAA15 most likely is intact. Surprisingly, the NatA activity of NAA10 Ile72Thr appears normal while its monomeric activity is decreased. This study further broadens the phenotypic spectrum associated with NAA10 deficiency, and adds to the evidence that genotype-phenotype correlations for NAA10 variants are much more complex than initially anticipated.
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13
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DTNB-Based Quantification of In Vitro Enzymatic N-Terminal Acetyltransferase Activity. Methods Mol Biol 2018; 1574:9-15. [PMID: 28315240 DOI: 10.1007/978-1-4939-6850-3_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We here describe a quick and easy method to quantitatively measure in vitro acetylation activity of not only N-terminal acetyltransferase (NAT) enzymes, but acetyltransferases using acetyl-coenzyme A as an acetyl donor in general.
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14
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Varland S, Myklebust LM, Goksøyr SØ, Glomnes N, Torsvik J, Varhaug JE, Arnesen T. Identification of an alternatively spliced nuclear isoform of human N-terminal acetyltransferase Naa30. Gene 2017; 644:27-37. [PMID: 29247799 DOI: 10.1016/j.gene.2017.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022]
Abstract
N-terminal acetylation is a highly abundant and important protein modification in eukaryotes catalyzed by N-terminal acetyltransferases (NATs). In humans, six different NATs have been identified (NatA-NatF), each composed of individual subunits and acetylating a distinct set of substrates. Along with most NATs, NatC acts co-translationally at the ribosome. The NatC complex consists of the catalytic subunit Naa30 and the auxiliary subunits Naa35 and Naa38, and can potentially Nt-acetylate cytoplasmic proteins when the initiator methionine is followed by a bulky hydrophobic/amphipathic residue at position 2. Here, we have identified a splice variant of human NAA30, which encodes a truncated protein named Naa30288. The splice variant was abundantly present in thyroid cancer tissues and in several different human cancer cell lines. Surprisingly, Naa30288 localized predominantly to the nucleus, as opposed to annotated Naa30 which has a cytoplasmic localization. Full-length Naa30 acetylated a classical NatC substrate peptide in vitro, whereas no significant NAT activity was detected for Naa30288. Due to the nuclear localization, we also examined acetyltransferase activity towards lysine residues. Neither full-length Naa30 nor Naa30288 displayed any lysine acetyltransferase activity. Overexpression of full-length Naa30 increased cell viability via inhibition of apoptosis. In contrast, Naa30288 did not exert an anti-apoptotic effect. In sum, we identified a novel and widely expressed Naa30 isoform with a potential non-catalytic role in the nucleus.
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Affiliation(s)
- Sylvia Varland
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Siri Øfsthus Goksøyr
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Nina Glomnes
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway; Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5021 Bergen, Norway
| | - Janniche Torsvik
- Department of Neurology, Haukeland University Hospital, Jonas Lies vei 87, 5021 Bergen, Norway
| | - Jan Erik Varhaug
- Department of Surgery, Haukeland University Hospital, Jonas Lies vei 87, 5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway; Department of Surgery, Haukeland University Hospital, Jonas Lies vei 87, 5021 Bergen, Norway.
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