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Armbruster L, Pożoga M, Wu Z, Eirich J, Thulasi Devendrakumar K, De La Torre C, Miklánková P, Huber M, Bradic F, Poschet G, Weidenhausen J, Merker S, Ruppert T, Sticht C, Sinning I, Finkemeier I, Li X, Hell R, Wirtz M. Nα-acetyltransferase NAA50 mediates plant immunity independent of the Nα-acetyltransferase A complex. PLANT PHYSIOLOGY 2024; 195:3097-3118. [PMID: 38588051 DOI: 10.1093/plphys/kiae200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
In humans and plants, 40% of the proteome is cotranslationally acetylated at the N-terminus by a single Nα-acetyltransferase (Nat) termed NatA. The core NatA complex is comprised of the catalytic subunit Nα-acetyltransferase 10 (NAA10) and the ribosome-anchoring subunit NAA15. The regulatory subunit Huntingtin Yeast Partner K (HYPK) and the acetyltransferase NAA50 join this complex in humans. Even though both are conserved in Arabidopsis (Arabidopsis thaliana), only AtHYPK is known to interact with AtNatA. Here we uncover the AtNAA50 interactome and provide evidence for the association of AtNAA50 with NatA at ribosomes. In agreement with the latter, a split-luciferase approach demonstrated close proximity of AtNAA50 and AtNatA in planta. Despite their interaction, AtNatA/HYPK and AtNAA50 exerted different functions in vivo. Unlike NatA/HYPK, AtNAA50 did not modulate drought tolerance or promote protein stability. Instead, transcriptome and proteome analyses of a novel AtNAA50-depleted mutant (amiNAA50) implied that AtNAA50 negatively regulates plant immunity. Indeed, amiNAA50 plants exhibited enhanced resistance to oomycetes and bacterial pathogens. In contrast to what was observed in NatA-depleted mutants, this resistance was independent of an accumulation of salicylic acid prior to pathogen exposure. Our study dissects the in vivo function of the NatA interactors HYPK and NAA50 and uncovers NatA-independent roles for NAA50 in plants.
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Affiliation(s)
- Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marlena Pożoga
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Zhongshou Wu
- Michael Smith Laboratories, University of British Columbia, V6T1Z4 Vancouver, BC, Canada
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | | | - Carolina De La Torre
- NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Pavlina Miklánková
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Monika Huber
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Fabian Bradic
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jonas Weidenhausen
- Structural Biology, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Sabine Merker
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Ruppert
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University, 69120 Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Irmgard Sinning
- Structural Biology, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, V6T1Z4 Vancouver, BC, Canada
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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2
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François CM, Pihl T, Dunoyer de Segonzac M, Hérault C, Hudry B. Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction. Nat Commun 2023; 14:6737. [PMID: 37872135 PMCID: PMC10593830 DOI: 10.1038/s41467-023-42496-9] [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: 04/21/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The molecular mechanisms connecting cellular metabolism with differentiation remain poorly understood. Here, we find that metabolic signals contribute to stem cell differentiation and germline homeostasis during Drosophila melanogaster spermatogenesis. We discovered that external citrate, originating outside the gonad, fuels the production of Acetyl-coenzyme A by germline ATP-citrate lyase (dACLY). We show that this pathway is essential during the final spermatogenic stages, where a high Acetyl-coenzyme A level promotes NatB-dependent N-terminal protein acetylation. Using genetic and biochemical experiments, we establish that N-terminal acetylation shields key target proteins, essential for spermatid differentiation, from proteasomal degradation by the ubiquitin ligase dUBR1. Our work uncovers crosstalk between metabolism and proteome stability that is mediated via protein post-translational modification. We propose that this system coordinates the metabolic state of the organism with gamete production. More broadly, modulation of proteome turnover by circulating metabolites may be a conserved regulatory mechanism to control cell functions.
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Affiliation(s)
- Charlotte M François
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Thomas Pihl
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | | | - Chloé Hérault
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Bruno Hudry
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France.
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3
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Sugaya N, Tanaka S, Keyamura K, Noda S, Akanuma G, Hishida T. N-terminal acetyltransferase NatB regulates Rad51-dependent repair of double-strand breaks in Saccharomyces cerevisiae. Genes Genet Syst 2023; 98:61-72. [PMID: 37331807 DOI: 10.1266/ggs.23-00013] [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] [Indexed: 06/20/2023] Open
Abstract
Homologous recombination (HR) is a highly accurate mechanism for repairing DNA double-strand breaks (DSBs) that arise from various genotoxic insults and blocked replication forks. Defects in HR and unscheduled HR can interfere with other cellular processes such as DNA replication and chromosome segregation, leading to genome instability and cell death. Therefore, the HR process has to be tightly controlled. Protein N-terminal acetylation is one of the most common modifications in eukaryotic organisms. Studies in budding yeast implicate a role for NatB acetyltransferase in HR repair, but precisely how this modification regulates HR repair and genome integrity is unknown. In this study, we show that cells lacking NatB, a dimeric complex composed of Nat3 and Mdm2, are sensitive to the DNA alkylating agent methyl methanesulfonate (MMS), and that overexpression of Rad51 suppresses the MMS sensitivity of nat3Δ cells. Nat3-deficient cells have increased levels of Rad52-yellow fluorescent protein foci and fail to repair DSBs after release from MMS exposure. We also found that Nat3 is required for HR-dependent gene conversion and gene targeting. Importantly, we observed that nat3Δ mutation partially suppressed MMS sensitivity in srs2Δ cells and the synthetic sickness of srs2Δ sgs1Δ cells. Altogether, our results indicate that NatB functions upstream of Srs2 to activate the Rad51-dependent HR pathway for DSB repair.
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Affiliation(s)
- Natsuki Sugaya
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Shion Tanaka
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Shunsuke Noda
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Genki Akanuma
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
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4
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Pożoga M, Armbruster L, Wirtz M. From Nucleus to Membrane: A Subcellular Map of the N-Acetylation Machinery in Plants. Int J Mol Sci 2022; 23:ijms232214492. [PMID: 36430970 PMCID: PMC9692967 DOI: 10.3390/ijms232214492] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
N-terminal acetylation (NTA) is an ancient protein modification conserved throughout all domains of life. N-terminally acetylated proteins are present in the cytosol, the nucleus, the plastids, mitochondria and the plasma membrane of plants. The frequency of NTA differs greatly between these subcellular compartments. While up to 80% of cytosolic and 20-30% of plastidic proteins are subject to NTA, NTA of mitochondrial proteins is rare. NTA alters key characteristics of proteins such as their three-dimensional structure, binding properties and lifetime. Since the majority of proteins is acetylated by five ribosome-bound N-terminal acetyltransferases (Nats) in yeast and humans, NTA was long perceived as an exclusively co-translational process in eukaryotes. The recent characterization of post-translationally acting plant Nats, which localize to the plasma membrane and the plastids, has challenged this view. Moreover, findings in humans, yeast, green algae and higher plants uncover differences in the cytosolic Nat machinery of photosynthetic and non-photosynthetic eukaryotes. These distinctive features of the plant Nat machinery might constitute adaptations to the sessile lifestyle of plants. This review sheds light on the unique role of plant N-acetyltransferases in development and stress responses as well as their evolution-driven adaptation to function in different cellular compartments.
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5
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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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6
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Nyonda MA, Boyer JB, Belmudes L, Krishnan A, Pino P, Couté Y, Brochet M, Meinnel T, Soldati-Favre D, Giglione C. N-Acetylation of secreted proteins is widespread in Apicomplexa and independent of acetyl-CoA ER-transporter AT1. J Cell Sci 2022; 135:275539. [PMID: 35621049 DOI: 10.1242/jcs.259811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Acetyl-CoA participates in post-translational modification of proteins, central carbon and lipid metabolism in several cell compartments. In mammals, the acetyl-CoA transporter 1 (AT1) facilitates the flux of cytosolic acetyl-CoA into the endoplasmic reticulum (ER), enabling the acetylation of proteins of the secretory pathway, in concert with dedicated acetyltransferases including NAT8. However, the implication of the ER acetyl-CoA pool in acetylation of ER-transiting proteins in Apicomplexa is unknown. We identify homologues of AT1 and NAT8 in Toxoplasma gondii and Plasmodium berghei. Proteome-wide analyses revealed widespread N-terminal acetylation marks of secreted proteins in both parasites. Such acetylation profile of N-terminally processed proteins was never observed so far in any other organisms. AT1 deletion resulted in a considerable reduction of parasite fitness. In P. berghei, AT1 is important for growth of asexual blood stages and production of female gametocytes and male gametocytogenesis impaling its requirement for transmission. In the absence of AT1, the lysine and N-terminal acetylation sites remained globally unaltered, suggesting an uncoupling between the role of AT1 in development and active acetylation occurring along the secretory pathway.
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Affiliation(s)
- Mary Akinyi Nyonda
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Intergrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aarti Krishnan
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Paco Pino
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,ExcellGene SA, CH1870 Monthey, Switzerland
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Mathieu Brochet
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Intergrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Intergrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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7
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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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8
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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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9
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Ahmed F, Husain M. Human N-Alpha-Acetyltransferase 60 Promotes Influenza A Virus Infection by Dampening the Interferon Alpha Signaling. Front Immunol 2022; 12:771792. [PMID: 35095845 PMCID: PMC8790067 DOI: 10.3389/fimmu.2021.771792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
N-alpha-acetyltransferase 60 (NAA60) is the most recently discovered N-terminal acetyltransferase and found only in multicellular eukaryotes. NAA60 localizes to the Golgi complex and is one of the only two N-terminal acetyltransferases known to localize to an organelle. Furthermore, NAA60 possesses a unique ability of catalyzing the acetylation of membrane-anchored proteins at the N-terminus and histones at the lysine side chains. Herein, we demonstrate that NAA60 exhibits proviral properties during influenza A virus (IAV) infection by interfering with the interferon (IFN) α signaling. We found that the depletion and overexpression of NAA60 reduced and enhanced, respectively, the IAV growth in a cell type- and IAV strain-independent manner. Mechanistically, the IAV-induced expression of IFNα was increased and decreased in NAA60-depleted and -overexpressing cells, respectively. Furthermore, the depletion of NAA60 enhanced the level of phosphorylated STAT1 transcription factor as well as the expression of several IFN-stimulated genes (ISGs) such as MX1, CH25H, IFITM3, ISG15 and viperin in infected cells. Whereas the overexpression of NAA60 produced opposite results. Finally, similar results were obtained when the NAA60-depleted cells were treated with purified IFNα. These findings, in conjunction with our recent findings where N-terminal acetylation of many host proteins increased in response to the IAV infection, indicate an important role of N-terminal acetylation during IAV replication.
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10
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Huber M, Armbruster L, Etherington RD, De La Torre C, Hawkesford MJ, Sticht C, Gibbs DJ, Hell R, Wirtz M. Disruption of the N α-Acetyltransferase NatB Causes Sensitivity to Reductive Stress in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 12:799954. [PMID: 35046984 PMCID: PMC8761761 DOI: 10.3389/fpls.2021.799954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
In Arabidopsis thaliana, the evolutionary conserved N-terminal acetyltransferase (Nat) complexes NatA and NatB co-translationally acetylate 60% of the proteome. Both have recently been implicated in the regulation of plant stress responses. While NatA mediates drought tolerance, NatB is required for pathogen resistance and the adaptation to high salinity and high osmolarity. Salt and osmotic stress impair protein folding and result in the accumulation of misfolded proteins in the endoplasmic reticulum (ER). The ER-membrane resident E3 ubiquitin ligase DOA10 targets misfolded proteins for degradation during ER stress and is conserved among eukaryotes. In yeast, DOA10 recognizes conditional degradation signals (Ac/N-degrons) created by NatA and NatB. Assuming that this mechanism is preserved in plants, the lack of Ac/N-degrons required for efficient removal of misfolded proteins might explain the sensitivity of NatB mutants to protein harming conditions. In this study, we investigate the response of NatB mutants to dithiothreitol (DTT) and tunicamycin (TM)-induced ER stress. We report that NatB mutants are hypersensitive to DTT but not TM, suggesting that the DTT hypersensitivity is caused by an over-reduction of the cytosol rather than an accumulation of unfolded proteins in the ER. In line with this hypothesis, the cytosol of NatB depleted plants is constitutively over-reduced and a global transcriptome analysis reveals that their reductive stress response is permanently activated. Moreover, we demonstrate that doa10 mutants are susceptible to neither DTT nor TM, ruling out a substantial role of DOA10 in ER-associated protein degradation (ERAD) in plants. Contrary to previous findings in yeast, our data indicate that N-terminal acetylation (NTA) does not inhibit ER targeting of a substantial amount of proteins in plants. In summary, we provide further evidence that NatB-mediated imprinting of the proteome is vital for the response to protein harming stress and rule out DOA10 as the sole recognin for substrates in the plant ERAD pathway, leaving the role of DOA10 in plants ambiguous.
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Affiliation(s)
- Monika Huber
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
| | | | - Carolina De La Torre
- Institute of Clinical Chemistry, NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, Heidelberg, Germany
| | | | - Carsten Sticht
- Institute of Clinical Chemistry, NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, Heidelberg, Germany
| | - Daniel J. Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Rüdiger Hell
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
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11
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Asensio T, Dian C, Boyer JB, Rivière F, Meinnel T, Giglione C. A Continuous Assay Set to Screen and Characterize Novel Protein N-Acetyltransferases Unveils Rice General Control Non-repressible 5-Related N-Acetyltransferase2 Activity. FRONTIERS IN PLANT SCIENCE 2022; 13:832144. [PMID: 35273627 PMCID: PMC8902505 DOI: 10.3389/fpls.2022.832144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 05/19/2023]
Abstract
Protein N-acetyltransferases (NATs) belong to the general control non-repressible 5 (Gcn5)-related N-acetyltransferases (GNATs) superfamily. GNATs catalyze the transfer of acetyl from acetyl-CoA to the reactive amine moiety of a wide range of acceptors. NAT sequences are difficult to distinguish from other members of the GNAT superfamily and there are many uncharacterized GNATs. To facilitate the discovery and characterization of new GNATs, we have developed a new continuous, non-radioactive assay. This assay is virtually independent of the substrate and can be used to get substrate specificity hints. We validated first the assay with the well-characterized Schizosaccharomyces pombe NatA (SpNatA). The SpNatA kinetic parameters were determined with various peptides confirming the robustness of the new assay. We reveal that the longer the peptide substrate the more efficient the enzyme. As a proof of concept of the relevance of the new assay, we characterized a NAA90 member from rice (Oryza sativa), OsGNAT2. We took advantage of an in vivo medium-scale characterization of OsGNAT2 specificity to identify and then validate in vitro several specific peptide substrates. With this assay, we reveal long-range synergic effects of basic residues on OsGNAT2 activity. Overall, this new, high-throughput assay allows better understanding of the substrate specificity and activity of any GNAT.
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12
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Jespersen N, Monrroy L, Barandun J. Impact of Genome Reduction in Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:1-42. [PMID: 35543997 DOI: 10.1007/978-3-030-93306-7_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microsporidia represent an evolutionary outlier in the tree of life and occupy the extreme edge of the eukaryotic domain with some of their biological features. Many of these unicellular fungi-like organisms have reduced their genomic content to potentially the lowest limit. With some of the most compacted eukaryotic genomes, microsporidia are excellent model organisms to study reductive evolution and its functional consequences. While the growing number of sequenced microsporidian genomes have elucidated genome composition and organization, a recent increase in complementary post-genomic studies has started to shed light on the impacts of genome reduction in these unique pathogens. This chapter will discuss the biological framework enabling genome minimization and will use one of the most ancient and essential macromolecular complexes, the ribosome, to illustrate the effects of extreme genome reduction on a structural, molecular, and cellular level. We outline how reductive evolution in microsporidia has shaped DNA organization, the composition and function of the ribosome, and the complexity of the ribosome biogenesis process. Studying compacted mechanisms, processes, or macromolecular machines in microsporidia illuminates their unique lifestyle and provides valuable insights for comparative eukaryotic structural biology.
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Affiliation(s)
- Nathan Jespersen
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden.
| | - Leonardo Monrroy
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden.
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13
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Van Damme P. Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates. Int J Mol Sci 2021; 22:ijms221910692. [PMID: 34639033 PMCID: PMC8509067 DOI: 10.3390/ijms221910692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) catalyzed by conserved N-terminal acetyltransferases or NATs embodies a modification with one of the highest stoichiometries reported for eukaryotic protein modifications to date. Comprising the catalytic N-alpha acetyltransferase (NAA) subunit NAA10 plus the ribosome anchoring regulatory subunit NAA15, NatA represents the major acetyltransferase complex with up to 50% of all mammalian proteins representing potential substrates. Largely in consequence of the essential nature of NatA and its high enzymatic activity, its experimentally confirmed mammalian substrate repertoire remained poorly charted. In this study, human NatA knockdown conditions achieving near complete depletion of NAA10 and NAA15 expression resulted in lowered Nt-acetylation of over 25% out of all putative NatA targets identified, representing an up to 10-fold increase in the reported number of substrate N-termini affected upon human NatA perturbation. Besides pointing to less efficient NatA substrates being prime targets, several putative NatE substrates were shown to be affected upon human NatA knockdown. Intriguingly, next to a lowered expression of ribosomal proteins and proteins constituting the eukaryotic 48S preinitiation complex, steady-state levels of protein N-termini additionally point to NatA Nt-acetylation deficiency directly impacting protein stability of knockdown affected targets.
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Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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14
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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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15
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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16
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Ahmad A, Akram W, Bashir Z, Shahzadi I, Wang R, Abbas HMK, Hu D, Ahmed S, Xu X, Li G, Wu T. Functional and Structural Analysis of a Novel Acyltransferase from Pathogenic Phytophthora melonis. ACS OMEGA 2021; 6:1797-1808. [PMID: 33521421 PMCID: PMC7841795 DOI: 10.1021/acsomega.0c03186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 05/07/2023]
Abstract
This investigation characterizes an acyltransferase enzyme responsible for the pathogenicity of Phytophthora melonis. The protein was characterized in vitro for its physicochemical properties. The biochemical characterization, including thermal and pH stability, revealed the 35 °C temperature and 7.0 pH as the optimum conditions for the enzyme. Applying the Tween-80 solution enhanced the activity up to 124.9%. Comprehensive structural annotation revealed two domains, A (ranging from residues 260 to 620) and B (ranging from 141 to 219). Domain A had transglutaminase (T-Gase) elicitor properties, while B possessed antifreeze features. Rigorous sequence characterization of the acyltransferase tagged it as a low-temperature-resistant protein. Further, the taxonomic distribution analysis of the protein highlighted three genera in Oomycetes, i.e., Pythium, Phytophthora, and Plasmopara, bearing this protein. However, some taxonomic groups other than Oomycetes (i.e., archaea and bacteria) also contained the protein. Functional studies of structurally analogous proteins spanned 10 different taxonomic groups. These revealed TGase elicitors (10%), phytopathogen effector proteins RxLR (4%), transporter family proteins (3%), and endonucleases (1%). Other analogues having one percent of their individual share were HIV tat-specific factor 1, protocadherin fat 4, transcription factor 1, and 3-hydroxyisobutyrate dehydrogenase. Because the plant infection by P. melonis is a complex process regulated by a profusion of extracellular signals secreted by both host plants and the pathogen, this study will be of help in interpreting the cross-talk in the host-pathogen system.
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Affiliation(s)
- Aqeel Ahmad
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Waheed Akram
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Zoobia Bashir
- National
Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu 210093, China
| | - Iqra Shahzadi
- School
of Resource and Environmental Science, Wuhan
University, Wuhan 430072, Hubei, China
| | - Rui Wang
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Hafiz Muhammad Khalid Abbas
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Du Hu
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Shakeel Ahmed
- Instituto
de Farmacia, Facultad de Ciencias, Universidad
Austral de Chile, Campus
Isla Teja, Valdivia 5090000, Chile
| | - Xiaomei Xu
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Guihua Li
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Tingquan Wu
- Vegetable
Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong
Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
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17
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Krtenic B, Drazic A, Arnesen T, Reuter N. Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PLoS Comput Biol 2020; 16:e1007988. [PMID: 33362253 PMCID: PMC7790372 DOI: 10.1371/journal.pcbi.1007988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 01/07/2021] [Accepted: 10/16/2020] [Indexed: 11/19/2022] Open
Abstract
The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases. Enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily transfer an acetyl group from one molecule to another. This reaction is called acetylation and is one of the most common reactions inside the cell. The GNAT superfamily counts more than 870 000 members through all kingdoms of life. Despite sharing the same fold the GNAT superfamily is very diverse in terms of amino acid sequence and substrates. The eight N-terminal acetyltransferases (NatA, NatB, etc.. to NatH) are a GNAT subtype which acetylates the free amine group of polypeptide chains. This modification is called N-terminal acetylation and is one of the most abundant protein modifications in eukaryotic cells. This subtype is also characterized by a high sequence diversity even though they share the same substrate. In addition, the phylogeny of the superfamily is not characterized. This hampers functional annotation based on sequence similarity, and discovery of novel NATs. In this work we set out to solve the problem of the classification of eukaryotic GCN5-related acetyltransferases and report the first classification framework of the superfamily. This framework can be used as a tool for annotation of all GCN5-related acetyltransferases. As an example of what can be achieved we report in this paper the computational prediction and in vitro verification of the function of two previously uncharacterized N-terminal acetyltransferases. We also report the first acetyltransferase phylogenetic tree of the GCN5 superfamily. It indicates that N-terminal acetyltransferases do not constitute one homogeneous protein family, but that the ability to bind and acetylate protein N-termini had evolved more than once on the same acetylation scaffold. We also show that even small changes in key positions can lead to altered enzyme specificity.
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Affiliation(s)
- Bojan Krtenic
- Department of Biological Sciences, University of Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- * E-mail: (BK); (NR)
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, Norway
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Norway
- Department of Biomedicine, University of Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- Department of Chemistry, University of Bergen, Norway
- * E-mail: (BK); (NR)
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18
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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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19
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Linster E, Layer D, Bienvenut WV, Dinh TV, Weyer FA, Leemhuis W, Brünje A, Hoffrichter M, Miklankova P, Kopp J, Lapouge K, Sindlinger J, Schwarzer D, Meinnel T, Finkemeier I, Giglione C, Hell R, Sinning I, Wirtz M. The Arabidopsis N α -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response. THE NEW PHYTOLOGIST 2020; 228:554-569. [PMID: 32548857 DOI: 10.1111/nph.16747] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In humans and plants, N-terminal acetylation plays a central role in protein homeostasis, affects 80% of proteins in the cytoplasm and is catalyzed by five ribosome-associated N-acetyltransferases (NatA-E). Humans also possess a Golgi-associated NatF (HsNAA60) that is essential for Golgi integrity. Remarkably, NAA60 is absent in fungi and has not been identified in plants. Here we identify and characterize the first plasma membrane-anchored post-translationally acting N-acetyltransferase AtNAA60 in the reference plant Arabidopsis thaliana by the combined application of reverse genetics, global proteomics, live-cell imaging, microscale thermophoresis, circular dichroism spectroscopy, nano-differential scanning fluorometry, intrinsic tryptophan fluorescence and X-ray crystallography. We demonstrate that AtNAA60, like HsNAA60, is membrane-localized in vivo by an α-helical membrane anchor at its C-terminus, but in contrast to HsNAA60, AtNAA60 localizes to the plasma membrane. The AtNAA60 crystal structure provides insights into substrate-binding, the broad substrate specificity and the catalytic mechanism probed by structure-based mutagenesis. Characterization of the NAA60 loss-of-function mutants (naa60-1 and naa60-2) uncovers a plasma membrane-localized substrate of AtNAA60 and the importance of NAA60 during high salt stress. Our findings provide evidence for the plant-specific evolution of a plasma membrane-anchored N-acetyltransferase that is vital for adaptation to stress.
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Dominik Layer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Trinh V Dinh
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Felix A Weyer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Wiebke Leemhuis
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Marion Hoffrichter
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Ruediger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
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20
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Koufaris C, Kirmizis A. N-Terminal Acetyltransferases Are Cancer-Essential Genes Prevalently Upregulated in Tumours. Cancers (Basel) 2020; 12:E2631. [PMID: 32942614 PMCID: PMC7565035 DOI: 10.3390/cancers12092631] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
N-terminal acetylation (Nt-Ac) is an abundant eukaryotic protein modification, deposited in humans by one of seven N-terminal acetyltransferase (NAT) complexes composed of a catalytic and potentially auxiliary subunits. The involvement of NATs in cancers is being increasingly recognised, but a systematic cross-tumour assessment is currently lacking. To address this limitation, we conducted here a multi-omic data interrogation for NATs. We found that tumour genomic alterations of NATs or of their protein substrates are generally rare events, with some tumour-specific exceptions. In contrast, altered gene expression of NATs in cancers and their association with patient survival constitute a widespread cancer phenomenon. Examination of dependency screens revealed that (i), besides NAA60 and NAA80 and the NatA paralogues NAA11 and NAA16, the other ten NAT genes were within the top 80th percentile of the most dependent genes (ii); NATs act through distinct biological processes. NAA40 (NatD) emerged as a NAT with particularly interesting cancer biology and therapeutic potential, especially in liver cancer where a novel oncogenic role was supported by its increased expression in multiple studies and its association with patient survival. In conclusion, this study generated insights and data that will be of great assistance in guiding further research into the function and therapeutic potential of NATs in cancer.
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Affiliation(s)
- Costas Koufaris
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
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21
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Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation. Trends Biochem Sci 2020; 46:15-27. [PMID: 32912665 DOI: 10.1016/j.tibs.2020.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022]
Abstract
N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.
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22
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Armbruster L, Linster E, Boyer JB, Brünje A, Eirich J, Stephan I, Bienvenut WV, Weidenhausen J, Meinnel T, Hell R, Sinning I, Finkemeier I, Giglione C, Wirtz M. NAA50 Is an Enzymatically Active N α-Acetyltransferase That Is Crucial for Development and Regulation of Stress Responses. PLANT PHYSIOLOGY 2020; 183:1502-1516. [PMID: 32461302 PMCID: PMC7401105 DOI: 10.1104/pp.20.00222] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/15/2020] [Indexed: 05/11/2023]
Abstract
Nα-terminal acetylation (NTA) is a prevalent protein modification in eukaryotes. In plants, the biological function of NTA remains enigmatic. The dominant N-acetyltransferase (Nat) in Arabidopsis (Arabidopsis thaliana) is NatA, which cotranslationally catalyzes acetylation of ∼40% of the proteome. The core NatA complex consists of the catalytic subunit NAA10 and the ribosome-anchoring subunit NAA15. In human (Homo sapiens), fruit fly (Drosophila melanogaster), and yeast (Saccharomyces cerevisiae), this core NatA complex interacts with NAA50 to form the NatE complex. While in metazoa, NAA50 has N-acetyltransferase activity, yeast NAA50 is catalytically inactive and positions NatA at the ribosome tunnel exit. Here, we report the identification and characterization of Arabidopsis NAA50 (AT5G11340). Consistent with its putative function as a cotranslationally acting Nat, AtNAA50-EYFP localized to the cytosol and the endoplasmic reticulum but also to the nuclei. We demonstrate that purified AtNAA50 displays Nα-terminal acetyltransferase and lysine-ε-autoacetyltransferase activity in vitro. Global N-acetylome profiling of Escherichia coli cells expressing AtNAA50 revealed conservation of NatE substrate specificity between plants and humans. Unlike the embryo-lethal phenotype caused by the absence of AtNAA10 and AtNAA15, loss of NAA50 expression resulted in severe growth retardation and infertility in two Arabidopsis transfer DNA insertion lines (naa50-1 and naa50-2). The phenotype of naa50-2 was rescued by the expression of HsNAA50 or AtNAA50. In contrast, the inactive ScNAA50 failed to complement naa50-2 Remarkably, loss of NAA50 expression did not affect NTA of known NatA substrates and caused the accumulation of proteins involved in stress responses. Overall, our results emphasize a relevant role of AtNAA50 in plant defense and development, which is independent of the essential NatA activity.
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Affiliation(s)
- Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Annika Brünje
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | | | - Thierry Meinnel
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Carmela Giglione
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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23
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Bienvenut WV, Brünje A, Boyer J, Mühlenbeck JS, Bernal G, Lassowskat I, Dian C, Linster E, Dinh TV, Koskela MM, Jung V, Seidel J, Schyrba LK, Ivanauskaite A, Eirich J, Hell R, Schwarzer D, Mulo P, Wirtz M, Meinnel T, Giglione C, Finkemeier I. Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation. Mol Syst Biol 2020; 16:e9464. [PMID: 32633465 PMCID: PMC7339202 DOI: 10.15252/msb.20209464] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-α-acetylation (NTA) and ε-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5-related N-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.
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Affiliation(s)
- Willy V Bienvenut
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Génétique Quantitative et ÉvolutionGif‐sur‐YvetteFrance
| | - Annika Brünje
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Jean‐Baptiste Boyer
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jens S Mühlenbeck
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Gautier Bernal
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute of Plant Sciences Paris‐SaclayGif‐sur‐YvetteFrance
| | - Ines Lassowskat
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Cyril Dian
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Eric Linster
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Trinh V Dinh
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Minna M Koskela
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
- Present address:
Institute of MicrobiologyTřeboňCzech Republic
| | - Vincent Jung
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute IMAGINEParisFrance
| | - Julian Seidel
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Laura K Schyrba
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Aiste Ivanauskaite
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Jürgen Eirich
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Rüdiger Hell
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Dirk Schwarzer
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Paula Mulo
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Markus Wirtz
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Thierry Meinnel
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Carmela Giglione
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Iris Finkemeier
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
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24
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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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25
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Abboud A, Bédoucha P, Byška J, Arnesen T, Reuter N. Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases. Comput Struct Biotechnol J 2020; 18:532-547. [PMID: 32206212 PMCID: PMC7078549 DOI: 10.1016/j.csbj.2020.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
N-terminal acetyltransferases (NATs) belong to the superfamily of acetyltransferases. They are enzymes catalysing the transfer of an acetyl group from acetyl coenzyme A to the N-terminus of polypeptide chains. N-terminal acetylation is one of the most common protein modifications. To date, not much is known on the molecular basis for the exclusive substrate specificity of NATs. All NATs share a common fold called GNAT. A characteristic of NATs is the β6β7 hairpin loop covering the active site and forming with the α1α2 loop a narrow tunnel surrounding the catalytic site in which cofactor and polypeptide meet and exchange an acetyl group. We investigated the dynamics-function relationships of all available structures of NATs covering the three domains of Life. Using an elastic network model and normal mode analysis, we found a common dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove formed by the β4 and β5 strands and splitting the fold in two dynamical subdomains. Loops α1α2, β3β4 and β6β7 all show clear displacements in the low frequency normal modes. We characterized the mobility of the loops and show that even limited conformational changes of the loops along the low-frequency modes are able to significantly change the size and shape of the ligand binding sites. Based on the fact that these movements are present in most low-frequency modes, and common to all NATs, we suggest that the α1α2 and β6β7 loops may regulate ligand uptake and the release of the acetylated polypeptide.
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Affiliation(s)
- Angèle Abboud
- Department of Informatics, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pierre Bédoucha
- Department of Informatics, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jan Byška
- Department of Informatics, University of Bergen, Bergen, Norway
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
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26
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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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27
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Sharma S, Ahmed M, Akhter Y. Fungal acetyltransferases structures, mechanisms and inhibitors: A review. Int J Biol Macromol 2019; 157:626-640. [PMID: 31786301 DOI: 10.1016/j.ijbiomac.2019.11.214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Acetylation of proteins is vital and mediate many processes within the cells like protein interactions, intercellular localization, protein stability, transcriptional regulation, enzyme activity and many more. Acetylation, an evolutionarily conserved process, attracted more attention due to its key regulatory role in many cellular processes and its effect on proteome and metabolome. In eukaryotes, protein acetylation also contribute to the epigenetic regulation of gene expression. Acetylation involves the transfer of acetyl group from donor acetyl coenzyme A to a suitable acceptor molecule and the reaction is catalyzed by acetyltransferase enzymes. The review focuses on current understanding of different acetyltransferase families: their discovery, structure and catalytic mechanism in fungal species. Fungal acetyltransferases use divergent catalytic mechanisms and carry out catalysis in a substrate-specific manner. The studies have explored different fungal acetyltransferases in relation to secondary metabolite production and the fungal pathogenesis. Although, the functions and catalytic mechanism of acetyltransferases are well known, however further enhanced knowledge may improve their utilization in various applications of biotechnology.
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Affiliation(s)
- Shikha Sharma
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Mushtaq Ahmed
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
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28
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Eldeeb MA, Fahlman RP, Ragheb MA, Esmaili M. Does N‐Terminal Protein Acetylation Lead to Protein Degradation? Bioessays 2019; 41:e1800167. [DOI: 10.1002/bies.201800167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 08/12/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mohamed A. Eldeeb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill University Montreal Quebec H3A 2B4 Canada
| | - Richard P. Fahlman
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
| | - Mohamed A. Ragheb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
| | - Mansoore Esmaili
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
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29
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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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30
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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31
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Elías-Villalobos A, Barrales RR, Ibeas JI. Chromatin modification factors in plant pathogenic fungi: Insights from Ustilago maydis. Fungal Genet Biol 2019; 129:52-64. [PMID: 30980908 DOI: 10.1016/j.fgb.2019.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 01/10/2023]
Abstract
Adaptation to the environment is a requirement for the survival of every organism. For pathogenic fungi this also implies coping with the different conditions that occur during the infection cycle. After detecting changes to external media, organisms must modify their gene expression patterns in order to accommodate the new circumstances. Control of gene expression is a complex process that involves the coordinated action of multiple regulatory elements. Chromatin modification is a well-known mechanism for controlling gene expression in response to environmental changes in all eukaryotes. In pathogenic fungi, chromatin modifications are known to play crucial roles in controlling host interactions and their virulence capacity, yet little is known about the specific genes they directly target and to which signals they respond. The smut fungus Ustilago maydis is an excellent model system in which multiple molecular and cellular approaches are available to study biotrophic interactions. Many target genes regulated during the infection process have been well studied, however, how they are controlled and specifically how chromatin modifications affect gene regulation in the context of infection is not well known in this organism. Here, we analyse the presence of chromatin modifying enzymes and complexes in U. maydis and discuss their putative roles in this plant pathogen in the context of findings from other organisms, including other plant pathogens such as Magnaporthe oryzae and Fusarium graminearum. We propose U. maydis as a remarkable organism with interesting chromatin features, which would allow finding new functions of chromatin modifications during plant pathogenesis.
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Affiliation(s)
- Alberto Elías-Villalobos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR5237-Centre National de la Recherche Scientifique-Université de Montpellier, Montpellier, France.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain.
| | - José I Ibeas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
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32
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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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33
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Gottlieb L, Marmorstein R. Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Structure 2018; 26:925-935.e8. [PMID: 29754825 DOI: 10.1016/j.str.2018.04.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 12/31/2022]
Abstract
Co-translational N-terminal protein acetylation regulates many protein functions including degradation, folding, interprotein interactions, and targeting. Human NatA (hNatA), one of six conserved metazoan N-terminal acetyltransferases, contains Naa10 catalytic and Naa15 auxiliary subunits, and associates with the intrinsically disordered Huntingtin yeast two-hybrid protein K (HYPK). We report on the crystal structures of hNatA and hNatA/HYPK, and associated biochemical and enzymatic analyses. We demonstrate that hNatA contains unique features: a stabilizing inositol hexaphosphate (IP6) molecule and a metazoan-specific Naa15 domain that mediates high-affinity HYPK binding. We find that HYPK harbors intrinsic hNatA-specific inhibitory activity through a bipartite structure: a ubiquitin-associated domain that binds a hNaa15 metazoan-specific region and an N-terminal loop-helix region that distorts the hNaa10 active site. We show that HYPK binding blocks hNaa50 targeting to hNatA, likely limiting Naa50 ribosome localization in vivo. These studies provide a model for metazoan NAT activity and HYPK regulation of N-terminal acetylation.
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Affiliation(s)
- Leah Gottlieb
- 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.
| | - 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, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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34
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N-terminal acetylation modulates Bax targeting to mitochondria. Int J Biochem Cell Biol 2017; 95:35-42. [PMID: 29233735 DOI: 10.1016/j.biocel.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/28/2017] [Accepted: 12/06/2017] [Indexed: 01/13/2023]
Abstract
The pro-apoptotic Bax protein is the main effector of mitochondrial permeabilization during apoptosis. Bax is controlled at several levels, including post-translational modifications such as phosphorylation and S-palmitoylation. However, little is known about the contribution of other protein modifications to Bax activity. Here, we used heterologous expression of human Bax in yeast to study the involvement of N-terminal acetylation by yNaa20p (yNatB) on Bax function. We found that human Bax is N-terminal (Nt-)acetylated by yNaa20p and that Nt-acetylation of Bax is essential to maintain Bax in an inactive conformation in the cytosol of yeast and Mouse Embryonic Fibroblast (MEF) cells. Bax accumulates in the mitochondria of yeast naa20Δ and Naa25-/- MEF cells, but does not promote cytochrome c release, suggesting that an additional step is required for full activation of Bax. Altogether, our results show that Bax N-terminal acetylation by NatB is involved in its mitochondrial targeting.
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35
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Aksnes H, Goris M, Strømland Ø, Drazic A, Waheed Q, Reuter N, Arnesen T. Molecular determinants of the N-terminal acetyltransferase Naa60 anchoring to the Golgi membrane. J Biol Chem 2017; 292:6821-6837. [PMID: 28196861 DOI: 10.1074/jbc.m116.770362] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/29/2017] [Indexed: 11/06/2022] Open
Abstract
Nα-Acetyltransferase 60 (Naa60 or NatF) was recently identified as an unconventional N-terminal acetyltransferase (NAT) because it localizes to organelles, in particular the Golgi apparatus, and has a preference for acetylating N termini of the transmembrane proteins. This knowledge challenged the prevailing view of N-terminal acetylation as a co-translational ribosome-associated process and suggested a new mechanistic functioning for the enzymes responsible for this increasingly recognized protein modification. Crystallography studies on Naa60 were unable to resolve the C-terminal tail of Naa60, which is responsible for the organellar localization. Here, we combined modeling, in vitro assays, and cellular localization studies to investigate the secondary structure and membrane interacting capacity of Naa60. The results show that Naa60 is a peripheral membrane protein. Two amphipathic helices within the Naa60 C terminus bind the membrane directly in a parallel position relative to the lipid bilayer via hydrophobic and electrostatic interactions. A peptide corresponding to the C terminus was unstructured in solution and only folded into an α-helical conformation in the presence of liposomes. Computational modeling and cellular mutational analysis revealed the hydrophobic face of two α-helices to be critical for membranous localization. Furthermore, we found a strong and specific binding preference of Naa60 toward membranes containing the phosphatidylinositol PI(4)P, thus possibly explaining the primary residency of Naa60 at the PI(4)P-rich Golgi. In conclusion, we have defined the mode of cytosolic Naa60 anchoring to the Golgi apparatus, most likely occurring post-translationally and specifically facilitating post-translational N-terminal acetylation of many transmembrane proteins.
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Affiliation(s)
- Henriette Aksnes
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Marianne Goris
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Øyvind Strømland
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Adrian Drazic
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Qaiser Waheed
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen.,the Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, and
| | - Nathalie Reuter
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen.,the Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, and
| | - Thomas Arnesen
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen, .,the Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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36
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Staes A, Van Damme P, Timmerman E, Ruttens B, Stes E, Gevaert K, Impens F. Protease Substrate Profiling by N-Terminal COFRADIC. Methods Mol Biol 2017; 1574:51-76. [PMID: 28315243 DOI: 10.1007/978-1-4939-6850-3_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Detection of (neo-)N-terminal peptides is essential for identifying protease cleavage sites . We here present an update of a well-established and efficient selection method for enriching N-terminal peptides out of peptide mixtures: N-terminal COFRADIC (COmbined FRActional DIagonal Chromatography). This method is based on the old concept of diagonal chromatography, which involves a peptide modification step in between otherwise identical chromatographic separations, with this modification step finally allowing for the isolation of N-terminal peptides by longer retention of non-N-terminal peptides on the resin. N-terminal COFRADIC has been successfully applied in many protease-centric studies, as well as for studies on protein alpha-N-acetylation and on characterizing alternative translation initiation events.
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Affiliation(s)
- An Staes
- VIB Proteomics Core, B-9000, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Evy Timmerman
- VIB Proteomics Core, B-9000, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Bart Ruttens
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Elisabeth Stes
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Francis Impens
- VIB Proteomics Core, B-9000, Ghent, Belgium.
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium.
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium.
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Ribeiro AL, Silva RD, Foyn H, Tiago MN, Rathore OS, Arnesen T, Martinho RG. Naa50/San-dependent N-terminal acetylation of Scc1 is potentially important for sister chromatid cohesion. Sci Rep 2016; 6:39118. [PMID: 27996020 PMCID: PMC5171793 DOI: 10.1038/srep39118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/17/2016] [Indexed: 12/17/2022] Open
Abstract
The gene separation anxiety (san) encodes Naa50/San, a N-terminal acetyltransferase required for chromosome segregation during mitosis. Although highly conserved among higher eukaryotes, the mitotic function of this enzyme is still poorly understood. Naa50/San was originally proposed to be required for centromeric sister chromatid cohesion in Drosophila and human cells, yet, more recently, it was also suggested to be a negative regulator of microtubule polymerization through internal acetylation of beta Tubulin. We used genetic and biochemical approaches to clarify the function of Naa50/San during development. Our work suggests that Naa50/San is required during tissue proliferation for the correct interaction between the cohesin subunits Scc1 and Smc3. Our results also suggest a working model where Naa50/San N-terminally acetylates the nascent Scc1 polypeptide, and that this co-translational modification is subsequently required for the establishment and/or maintenance of sister chromatid cohesion.
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Affiliation(s)
- Ana Luisa Ribeiro
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Rui D Silva
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Håvard Foyn
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Margarida N Tiago
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Om Singh Rathore
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.,Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Rui Gonçalo Martinho
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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Romero-Meza G, Vélez-Ramírez DE, Florencio-Martínez LE, Román-Carraro FC, Manning-Cela R, Hernández-Rivas R, Martínez-Calvillo S. Maf1 is a negative regulator of transcription in Trypanosoma brucei. Mol Microbiol 2016; 103:452-468. [PMID: 27802583 DOI: 10.1111/mmi.13568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2016] [Indexed: 11/29/2022]
Abstract
RNA polymerase III (Pol III) produces small RNA molecules that play essential roles in mRNA processing and translation. Maf1, originally described as a negative regulator of Pol III transcription, has been studied from yeast to human. Here we characterized Maf1 in the parasitic protozoa Trypanosoma brucei (TbMaf1), representing the first report to analyse Maf1 in an early-diverged eukaryote. While Maf1 is generally encoded by a single-copy gene, the T. brucei genome contains two almost identical TbMaf1 genes. The TbMaf1 protein has the three conserved sequences and is predicted to fold into a globular structure. Unlike in yeast, TbMaf1 localizes to the nucleus in procyclic forms of T. brucei under normal growth conditions. Cell lines that either downregulate or overexpress TbMaf1 were generated, and growth curve analysis with them suggested that TbMaf1 participates in the regulation of cell growth of T. brucei. Nuclear run-on and chromatin immunoprecipitation analyses demonstrated that TbMaf1 represses Pol III transcription of tRNA and U2 snRNA genes by associating with their promoters. Interestingly, 5S rRNA levels do not change after TbMaf1 ablation or overexpression. Notably, our data also revealed that TbMaf1 regulates Pol I transcription of procyclin gene and Pol II transcription of SL RNA genes.
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Affiliation(s)
- Gabriela Romero-Meza
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México.,Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México, DF, 07360, México
| | - Daniel E Vélez-Ramírez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
| | - Fiordaliso C Román-Carraro
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
| | - Rebeca Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México, DF, 07360, México
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México, DF, 07360, México
| | - Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
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39
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Aksnes H, Drazic A, Marie M, Arnesen T. First Things First: Vital Protein Marks by N-Terminal Acetyltransferases. Trends Biochem Sci 2016; 41:746-760. [PMID: 27498224 DOI: 10.1016/j.tibs.2016.07.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/01/2016] [Accepted: 07/08/2016] [Indexed: 11/28/2022]
Abstract
N-terminal (Nt) acetylation is known to be a highly abundant co-translational protein modification, but the recent discovery of Golgi- and chloroplast-resident N-terminal acetyltransferases (NATs) revealed that it can also be added post-translationally. Nt-acetylation may act as a degradation signal in a novel branch of the N-end rule pathway, whose functions include the regulation of human blood pressure. Nt-acetylation also modulates protein interactions, targeting, and folding. In plants, Nt-acetylation plays a role in the control of resistance to drought and in regulation of immune responses. Mutations of specific human NATs that decrease their activity can cause either the lethal Ogden syndrome or severe intellectual disability and cardiovascular defects. In sum, recent advances highlight Nt-acetylation as a key factor in many biological pathways.
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Affiliation(s)
- Henriette Aksnes
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Adrian Drazic
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Michaël Marie
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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40
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Støve SI, Magin RS, Foyn H, Haug BE, Marmorstein R, Arnesen T. Crystal Structure of the Golgi-Associated Human Nα-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation. Structure 2016; 24:1044-56. [PMID: 27320834 DOI: 10.1016/j.str.2016.04.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 01/17/2023]
Abstract
N-Terminal acetylation is a common and important protein modification catalyzed by N-terminal acetyltransferases (NATs). Six human NATs (NatA-NatF) contain one catalytic subunit each, Naa10 to Naa60, respectively. In contrast to the ribosome-associated NatA to NatE, NatF/Naa60 specifically associates with Golgi membranes and acetylates transmembrane proteins. To gain insight into the molecular basis for the function of Naa60, we developed an Naa60 bisubstrate CoA-peptide conjugate inhibitor, determined its X-ray structure when bound to CoA and inhibitor, and carried out biochemical experiments. We show that Naa60 adapts an overall fold similar to that of the catalytic subunits of ribosome-associated NATs, but with the addition of two novel elongated loops that play important roles in substrate-specific binding. One of these loops mediates a dimer to monomer transition upon substrate-specific binding. Naa60 employs a catalytic mechanism most similar to Naa50. Collectively, these data reveal the molecular basis for Naa60-specific acetyltransferase activity with implications for its Golgi-specific functions.
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Affiliation(s)
- Svein Isungset Støve
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway
| | - Robert S Magin
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, PA 19104, USA
| | - Håvard Foyn
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Bengt Erik Haug
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, PA 19104, USA.
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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