1
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Lyon GJ, Longo J, Garcia A, Inusa F, Marchi E, Shi D, Dörfel M, Arnesen T, Aldabe R, Lyons S, Nashat MA, Bolton D. Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. PLoS One 2024; 19:e0301328. [PMID: 38713657 PMCID: PMC11075865 DOI: 10.1371/journal.pone.0301328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/14/2024] [Indexed: 05/09/2024] Open
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/y male mice on the inbred genetic background in this different animal facility.
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Affiliation(s)
- Gholson J. Lyon
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Joseph Longo
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Andrew Garcia
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Fatima Inusa
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Daniel Shi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Max Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, CIMA, University of Navarra, Pamplona, Spain
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Melissa A. Nashat
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - David Bolton
- Molecular Biology Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
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2
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Venezian J, Bar-Yosef H, Ben-Arie Zilberman H, Cohen N, Kleifeld O, Fernandez-Recio J, Glaser F, Shiber A. Diverging co-translational protein complex assembly pathways are governed by interface energy distribution. Nat Commun 2024; 15:2638. [PMID: 38528060 DOI: 10.1038/s41467-024-46881-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-protein interactions are at the heart of all cellular processes, with the ribosome emerging as a platform, orchestrating the nascent-chain interplay dynamics. Here, to study the characteristics governing co-translational protein folding and complex assembly, we combine selective ribosome profiling, imaging, and N-terminomics with all-atoms molecular dynamics. Focusing on conserved N-terminal acetyltransferases (NATs), we uncover diverging co-translational assembly pathways, where highly homologous subunits serve opposite functions. We find that only a few residues serve as "hotspots," initiating co-translational assembly interactions upon exposure at the ribosome exit tunnel. These hotspots are characterized by high binding energy, anchoring the entire interface assembly. Alpha-helices harboring hotspots are highly thermolabile, folding and unfolding during simulations, depending on their partner subunit to avoid misfolding. In vivo hotspot mutations disrupted co-translational complexation, leading to aggregation. Accordingly, conservation analysis reveals that missense NATs variants, causing neurodevelopmental and neurodegenerative diseases, disrupt putative hotspot clusters. Expanding our study to include phosphofructokinase, anthranilate synthase, and nucleoporin subcomplex, we employ AlphaFold-Multimer to model the complexes' complete structures. Computing MD-derived interface energy profiles, we find similar trends. Here, we propose a model based on the distribution of interface energy as a strong predictor of co-translational assembly.
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Affiliation(s)
- Johannes Venezian
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Hagit Bar-Yosef
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | | | - Noam Cohen
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Juan Fernandez-Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | - Fabian Glaser
- Lorry I. Lokey Interdisciplinary Center for Life Sciences & Engineering, Haifa, Israel
| | - Ayala Shiber
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel.
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3
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Lyon GJ, Longo J, Garcia A, Inusa F, Marchi E, Shi D, Dörfel M, Arnesen T, Aldabe R, Lyons S, Nashat MA, Bolton D. Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.27.538618. [PMID: 37163119 PMCID: PMC10168333 DOI: 10.1101/2023.04.27.538618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/Y male mice on the inbred genetic background in this different animal facility.
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Affiliation(s)
- Gholson J. Lyon
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, USA
| | - Joseph Longo
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Andrew Garcia
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, USA
| | - Fatima Inusa
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Elaine Marchi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Daniel Shi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Max Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, 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
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, CIMA, University of Navarra, Pamplona, Spain
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, USA
| | - Melissa A. Nashat
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - David Bolton
- Molecular Biology Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
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4
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Sandomirsky K, Marchi E, Gavin M, Amble K, Lyon GJ. Phenotypic variability and gastrointestinal manifestations/interventions for growth in NAA10-related neurodevelopmental syndrome. Am J Med Genet A 2023; 191:1293-1300. [PMID: 36810866 PMCID: PMC10364991 DOI: 10.1002/ajmg.a.63152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/23/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
Our study of 61 children with NAA10-related neurodevelopmental syndrome, an X-linked disorder due to NAA10 gene variants, demonstrated a high prevalence of growth failure, with weight and height percentiles often in the failure-to-thrive diagnostic range; however, dramatic weight fluctuations and phenotypic variability is evidenced in the growth parameters of this population. Although never previously explored in depth, the gastrointestinal pathology associated with NAA10-related neurodevelopmental syndrome includes feeding difficulties in infancy, dysphagia, GERD/silent reflux, vomiting, constipation, diarrhea, bowel incontinence, and presence of eosinophils on esophageal endoscopy, in order from most to least prevalent. Additionally, the gastrointestinal symptom profile for children with this syndrome has been expanded to include eosinophilic esophagitis, cyclic vomiting syndrome, Mallory Weiss tears, abdominal migraine, esophageal dilation, and subglottic stenosis. Although the exact cause of poor growth in NAA10-related neurodevelopmental syndrome probands is unclear and the degree of contribution to this problem by GI symptomatology remains uncertain, an analysis including nine G-tube or GJ-tube fed probands demonstrates that G/GJ-tubes are overall efficacious with respect to improvements in weight gain and caregiving. The choice to insert a gastrostomy or gastrojejunal tube to aid with weight gain is often a challenging decision to make for parents, who may alternatively choose to rely on oral feeding, caloric supplementation, calorie tracking, and feeding therapy. In this case, if NAA10-related neurodevelopmental syndrome children are not tracking above the failure to thrive (FTT) range past 1 year of age despite such efforts, the treating physicians should be consulted regarding possibly undergoing G-tube placement to avoid prolonged growth failure. If G-tubes are not immediately inducing weight gain after insertion, recommendations could include altering formula, increasing caloric input, or exchanging a G-tube for a GJ-tube by means of a minimally invasive procedure.
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Affiliation(s)
- Katherine Sandomirsky
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
| | - Maureen Gavin
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
| | - Karen Amble
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
| | - Gholson J. Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, New York, USA
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5
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Schuster R, Okamoto K. An overview of the molecular mechanisms of mitophagy in yeast. Biochim Biophys Acta Gen Subj 2022; 1866:130203. [PMID: 35842014 DOI: 10.1016/j.bbagen.2022.130203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/27/2022] [Accepted: 07/11/2022] [Indexed: 11/18/2022]
Abstract
Autophagy-dependent selective degradation of excess or damaged mitochondria, termed mitophagy, is a tightly regulated process necessary for mitochondrial quality and quantity control. Mitochondria are highly dynamic and major sites for vital cellular processes such as ATP and iron‑sulfur cluster biogenesis. Due to their pivotal roles for immunity, apoptosis, and aging, the maintenance of mitochondrial function is of utmost importance for cellular homeostasis. In yeast, mitophagy is mediated by the receptor protein Atg32 that is localized to the outer mitochondrial membrane. Upon mitophagy induction, Atg32 expression is transcriptionally upregulated, which leads to its accumulation on the mitochondrial surface and to recruitment of the autophagic machinery via its direct interaction with Atg11 and Atg8. Importantly, post-translational modifications such as phosphorylation further fine-tune the mitophagic response. This review summarizes the current knowledge about mitophagy in yeast and its connection with mitochondrial dynamics and the ubiquitin-proteasome system.
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Affiliation(s)
- Ramona Schuster
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Koji Okamoto
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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6
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Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez‐Mendez B, Sotelo‐Parrilla P, Jeyaprakash AA, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. Chemogenetic profiling reveals PP2A-independent cytotoxicity of proposed PP2A activators iHAP1 and DT-061. EMBO J 2022; 41:e110611. [PMID: 35695070 PMCID: PMC9289710 DOI: 10.15252/embj.2022110611] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The compounds iHAP1 and DT-061 have recently been reported to selectively stabilize specific PP2A-B56 complexes to mediate cell killing. We were unable to detect direct effects of iHAP1 and DT-061 on PP2A-B56 activity in biochemical assays and composition of holoenzymes. Therefore, we undertook genome-wide CRISPR-Cas9 synthetic lethality screens to uncover biological pathways affected by these compounds. We found that knockout of mitotic regulators is synthetic lethal with iHAP1 while knockout of endoplasmic reticulum (ER) and Golgi components is synthetic lethal with DT-061. Indeed we showed that iHAP1 directly blocks microtubule assembly both in vitro and in vivo and thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the ER and lipid synthesis associated with these structures. Our work provides insight into the biological pathways perturbed by iHAP1 and DT-061 causing cellular toxicity and argues that these compounds cannot be used for dissecting PP2A-B56 biology.
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Affiliation(s)
- Gianmatteo Vit
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Joana Duro
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Girish Rajendraprasad
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark
| | - Emil P T Hertz
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Lya Katrine Kauffeldt Holland
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Brennan C McEwan
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA,Norris Cotton Cancer CenterLebanonNHUSA
| | - Blanca Lopez‐Mendez
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kenji Maeda
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Arminja Kettenbach
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Marin Barisic
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark,Department of Cellular and Molecular MedicineFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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7
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Ma H, Li L, Gai Y, Zhang X, Chen Y, Zhuo X, Cao Y, Jiao C, Gmitter FG, Li H. Histone Acetyltransferases and Deacetylases Are Required for Virulence, Conidiation, DNA Damage Repair, and Multiple Stresses Resistance of Alternaria alternata. Front Microbiol 2021; 12:783633. [PMID: 34880849 PMCID: PMC8645686 DOI: 10.3389/fmicb.2021.783633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/02/2021] [Indexed: 01/16/2023] Open
Abstract
Histone acetylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by HATs and HDACs. This study determined the function of 6 histone acetyltransferases (HATs) (Gcn5, RTT109, Elp3, Sas3, Sas2, Nat3) and 6 histone deacetylases (HDACs) (Hos2, Rpd3, Hda1, Hos3, Hst2, Sir2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. Our data provide evidence that HATs and HDACs are both required for mycelium growth, cell development and pathogenicity as many gene deletion mutants (ΔGcn5, ΔRTT109, ΔElp3, ΔSas3, ΔNat3, ΔHos2, and ΔRpd3) displayed reduced growth, conidiation or virulence at varying degrees. In addition, HATs and HDACs are involved in the resistance to multiple stresses such as oxidative stress (Sas3, Gcn5, Elp3, RTT109, Hos2), osmotic stress (Sas3, Gcn5, RTT109, Hos2), cell wall-targeting agents (Sas3, Gcn5, Hos2), and fungicide (Gcn5, Hos2). ΔGcn5, ΔSas3, and ΔHos2 displayed severe growth defects on sole carbon source medium suggesting a vital role of HATs and HDACs in carbon source utilization. More SNPs were generated in ΔGcn5 in comparison to wild-type when they were exposed to ultraviolet ray. Moreover, ΔRTT109, ΔGcn5, and ΔHos2 showed severe defects in resistance to DNA-damaging agents, indicating the critical role of HATs and HDACs in DNA damage repair. These phenotypes correlated well with the differentially expressed genes in ΔGcn5 and ΔHos2 that are essential for carbon sources metabolism, DNA damage repair, ROS detoxification, and asexual development. Furthermore, Gcn5 is required for the acetylation of H3K4. Overall, our study provides genetic evidence to define the central role of HATs and HDACs in the pathological and biological functions of A. alternata.
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Affiliation(s)
- Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China.,Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Zhang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanan Chen
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaokang Zhuo
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yingzi Cao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chen Jiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fred G Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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8
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Kweon HY, Lee MN, Dorfel M, Seo S, Gottlieb L, PaPazyan T, McTiernan N, Ree R, Bolton D, Garcia A, Flory M, Crain J, Sebold A, Lyons S, Ismail A, Marchi E, Sonn SK, Jeong SJ, Jeon S, Ju S, Conway SJ, Kim T, Kim HS, Lee C, Roh TY, Arnesen T, Marmorstein R, Oh GT, Lyon GJ. Naa12 compensates for Naa10 in mice in the amino-terminal acetylation pathway. eLife 2021; 10:e65952. [PMID: 34355692 PMCID: PMC8376253 DOI: 10.7554/elife.65952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 08/05/2021] [Indexed: 01/17/2023] Open
Abstract
Amino-terminal acetylation is catalyzed by a set of N-terminal acetyltransferases (NATs). The NatA complex (including X-linked Naa10 and Naa15) is the major acetyltransferase, with 40-50% of all mammalian proteins being potential substrates. However, the overall role of amino-terminal acetylation on a whole-organism level is poorly understood, particularly in mammals. Male mice lacking Naa10 show no globally apparent in vivo amino-terminal acetylation impairment and do not exhibit complete embryonic lethality. Rather Naa10 nulls display increased neonatal lethality, and the majority of surviving undersized mutants exhibit a combination of hydrocephaly, cardiac defects, homeotic anterior transformation, piebaldism, and urogenital anomalies. Naa12 is a previously unannotated Naa10-like paralog with NAT activity that genetically compensates for Naa10. Mice deficient for Naa12 have no apparent phenotype, whereas mice deficient for Naa10 and Naa12 display embryonic lethality. The discovery of Naa12 adds to the currently known machinery involved in amino-terminal acetylation in mice.
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Affiliation(s)
- Hyae Yon Kweon
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Mi-Ni Lee
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
- Laboratory Animal Resource Center Korea ResearchInstitute of Bioscience and BiotechnologyChungbukRepublic of Korea
| | - Max Dorfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Seungwoon Seo
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Leah Gottlieb
- Department of Chemistry, University of PennsylvaniaPhiladelphiaUnited States
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Thomas PaPazyan
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Nina McTiernan
- Department of Biomedicine, University of BergenBergenNorway
| | - Rasmus Ree
- Department of Biomedicine, University of BergenBergenNorway
| | - David Bolton
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Andrew Garcia
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Michael Flory
- Research Design and Analysis Service, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Alison Sebold
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Ahmed Ismail
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Seong-keun Sonn
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Se-Jin Jeong
- Center for Cardiovascular Research, Washington University School of MedicineSaint LouisUnited States
| | - Sejin Jeon
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and TechnologySeoulRepublic of Korea
| | - Simon J Conway
- Herman B. Wells Center for Pediatric Research, Indiana University School of MedicineIndianapolisUnited States
| | - Taesoo Kim
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Hyun-Seok Kim
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and TechnologySeoulRepublic of Korea
- Department of Converging Science and Technology, KHU-KIST, Kyung Hee UniversitySeoulRepublic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and TechnologyPohangRepublic of Korea
| | - Thomas Arnesen
- Department of Biomedicine, University of BergenBergenNorway
- Department of Biological Sciences, University of BergenBergenNorway
- Department of Surgery, Haukeland University HospitalBergenNorway
| | - Ronen Marmorstein
- Department of Chemistry, University of PennsylvaniaPhiladelphiaUnited States
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Goo Taeg Oh
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
- Biology PhD Program, The Graduate Center, The City University of New YorkNew YorkUnited States
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
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9
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N α-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae. Cell Rep 2021; 34:108711. [PMID: 33535049 DOI: 10.1016/j.celrep.2021.108711] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 10/10/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022] Open
Abstract
N-terminal (Nt) acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt acetyltransferases (Nats) with differing specificities. Nt acetylation has been implicated in protein quality control, but its broad biological significance remains elusive. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAΔ and natBΔ mutants. Our results reveal a range of NatA- and NatB-specific phenotypes. NatA is implicated in systemic adaptation control, because natAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes, and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, because natBΔ mutants, to a greater extent than natA mutants, accumulate protein aggregates, induce stress responses, and display reduced fitness in the absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.
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10
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Jung TY, Ryu JE, Jang MM, Lee SY, Jin GR, Kim CW, Lee CY, Kim H, Kim E, Park S, Lee S, Lee C, Kim W, Kim T, Lee SY, Ju BG, Kim HS. Naa20, the catalytic subunit of NatB complex, contributes to hepatocellular carcinoma by regulating the LKB1-AMPK-mTOR axis. Exp Mol Med 2020; 52:1831-1844. [PMID: 33219302 PMCID: PMC8080711 DOI: 10.1038/s12276-020-00525-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
N-α-acetyltransferase 20 (Naa20), which is a catalytic subunit of the N-terminal acetyltransferase B (NatB) complex, has recently been reported to be implicated in hepatocellular carcinoma (HCC) progression and autophagy, but the underlying mechanism remains unclear. Here, we report that based on bioinformatic analysis of Gene Expression Omnibus and The Cancer Genome Atlas data sets, Naa20 expression is much higher in HCC tumors than in normal tissues, promoting oncogenic properties in HCC cells. Mechanistically, Naa20 inhibits the activity of AMP-activated protein kinase (AMPK) to promote the mammalian target of rapamycin signaling pathway, which contributes to cell proliferation, as well as autophagy, through its N-terminal acetyltransferase (NAT) activity. We further show that liver kinase B1 (LKB1), a major regulator of AMPK activity, can be N-terminally acetylated by NatB in vitro, but also probably by NatB and/or other members of the NAT family in vivo, which may have a negative effect on AMPK activity through downregulation of LKB1 phosphorylation at S428. Indeed, p-LKB1 (S428) and p-AMPK levels are enhanced in Naa20-deficient cells, as well as in cells expressing the nonacetylated LKB1-MPE mutant; moreover, importantly, LKB1 deficiency reverses the molecular and cellular events driven by Naa20 knockdown. Taken together, our findings suggest that N-terminal acetylation of LKB1 by Naa20 may inhibit the LKB1-AMPK signaling pathway, which contributes to tumorigenesis and autophagy in HCC.
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Affiliation(s)
- Taek-Yeol Jung
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea.,Department of Life Science, College of Natural Science, Sogang University, Seoul, 04107, South Korea
| | - Jae-Eun Ryu
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Mi-Mi Jang
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Soh-Yeon Lee
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Gyu-Rin Jin
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Chan-Woo Kim
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea.,Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Chae-Young Lee
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea
| | - Hyelee Kim
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea
| | - EungHan Kim
- Department of Biochemistry, College of Natural Science, Chungbuk National University, Cheongju, 28644, South Korea
| | - Sera Park
- KaiPharm, Seoul, 03759, Republic of Korea
| | - Seonjeong Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, South Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, South Korea.,Department of Converging Science and Technology, KHU-KIST, Kyung Hee University, Seoul, 02447, South Korea
| | - Wankyu Kim
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea.,KaiPharm, Seoul, 03759, Republic of Korea
| | - TaeSoo Kim
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea.,The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, 03760, South Korea
| | - Soo-Young Lee
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea.,The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, 03760, South Korea
| | - Bong-Gun Ju
- Department of Life Science, College of Natural Science, Sogang University, Seoul, 04107, South Korea
| | - Hyun-Seok Kim
- Department of Life Science, College of Natural Science, Ewha Womans University, Seoul, 03760, South Korea. .,Department of Bioinspired Science, Ewha Womans University, Seoul, 03760, South Korea. .,The Fluorescence Core Imaging Center, Ewha Womans University, Seoul, 03760, South Korea.
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11
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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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12
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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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13
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Wai A, Shen C, Carta A, Dansen A, Crous PW, Hausner G. Intron-encoded ribosomal proteins and N-acetyltransferases within the mitochondrial genomes of fungi: here today, gone tomorrow? Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:573-584. [DOI: 10.1080/24701394.2019.1580272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Chen Shen
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Andrell Carta
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Alexandra Dansen
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Pedro W. Crous
- The Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, The Netherlands
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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14
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Fukuda T, Kanki T. Mechanisms and Physiological Roles of Mitophagy in Yeast. Mol Cells 2018; 41:35-44. [PMID: 29370687 PMCID: PMC5792711 DOI: 10.14348/molcells.2018.2214] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/08/2017] [Accepted: 12/05/2017] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are responsible for supplying of most of the cell's energy via oxidative phosphorylation. However, mitochondria also can be deleterious for a cell because they are the primary source of reactive oxygen species, which are generated as a byproduct of respiration. Accumulation of mitochondrial and cellular oxidative damage leads to diverse pathologies. Thus, it is important to maintain a population of healthy and functional mitochondria for normal cellular metabolism. Eukaryotes have developed defense mechanisms to cope with aberrant mitochondria. Mitochondria autophagy (known as mitophagy) is thought to be one such process that selectively sequesters dysfunctional or excess mitochondria within double-membrane autophagosomes and carries them into lysosomes/vacuoles for degradation. The power of genetics and conservation of fundamental cellular processes among eukaryotes make yeast an excellent model for understanding the general mechanisms, regulation, and function of mitophagy. In budding yeast, a mitochondrial surface protein, Atg32, serves as a mitochondrial receptor for selective autophagy that interacts with Atg11, an adaptor protein for selective types of autophagy, and Atg8, a ubiquitin-like protein localized to the isolation membrane. Atg32 is regulated transcriptionally and post-translationally to control mitophagy. Moreover, because Atg32 is a mitophagy-specific protein, analysis of its deficient mutant enables investigation of the physiological roles of mitophagy. Here, we review recent progress in the understanding of the molecular mechanisms and functional importance of mitophagy in yeast at multiple levels.
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Affiliation(s)
- Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510,
Japan
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510,
Japan
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15
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Kanyal A, Rawat M, Gurung P, Choubey D, Anamika K, Karmodiya K. Genome‐wide survey and phylogenetic analysis of histone acetyltransferases and histone deacetylases of
Plasmodium falciparum. FEBS J 2018; 285:1767-1782. [DOI: 10.1111/febs.14376] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/20/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Abhishek Kanyal
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | - Mukul Rawat
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | - Pratima Gurung
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | | | | | - Krishanpal Karmodiya
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
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16
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Weyer FA, Gumiero A, Lapouge K, Bange G, Kopp J, Sinning I. Structural basis of HypK regulating N-terminal acetylation by the NatA complex. Nat Commun 2017; 8:15726. [PMID: 28585574 PMCID: PMC5467210 DOI: 10.1038/ncomms15726] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/21/2017] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, N-terminal acetylation is one of the most common protein modifications involved in a wide range of biological processes. Most N-acetyltransferase complexes (NATs) act co-translationally, with the heterodimeric NatA complex modifying the majority of substrate proteins. Here we show that the Huntingtin yeast two-hybrid protein K (HypK) binds tightly to the NatA complex comprising the auxiliary subunit Naa15 and the catalytic subunit Naa10. The crystal structures of NatA bound to HypK or to a N-terminal deletion variant of HypK were determined without or with a bi-substrate analogue, respectively. The HypK C-terminal region is responsible for high-affinity interaction with the C-terminal part of Naa15. In combination with acetylation assays, the HypK N-terminal region is identified as a negative regulator of the NatA acetylation activity. Our study provides mechanistic insights into the regulation of this pivotal protein modification. N-terminal acetylation is a common eukaryotic protein modification that is primarily catalysed by the N-acetyl transferase complex A (NatA). Here, the authors present the crystal structure of NatA bound to Huntingtin yeast two-hybrid protein K (HypK) and show that HypK is a negative regulator of NatA.
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Affiliation(s)
- Felix Alexander Weyer
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Andrea Gumiero
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Gert Bange
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
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17
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18
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Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 525] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
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19
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McDowell G, Philpott A. New Insights Into the Role of Ubiquitylation of Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:35-88. [DOI: 10.1016/bs.ircmb.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Chang YY, Hsu CH. Multiple Conformations of the Loop Region Confers Heat-Resistance on SsArd1, a Thermophilic NatA. Chembiochem 2015; 17:214-7. [PMID: 26593285 DOI: 10.1002/cbic.201500568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Indexed: 11/10/2022]
Abstract
Structural comparison indicates that the loop region between β3 and β4 of SsArd1 is extended relative to the corresponding region in mesophilic Nats, and forms a plastic hydrogen-bond network mainly at two serine residues. Strikingly, two single-point mutants showed ∼3 °C decrease in melting temperature, and two other variants showed ∼7 °C decrease; this correlated with significantly reduced enzymatic activity. To our knowledge, this is the first discovery of a loop region capable of remarkably improving protein thermostability. This provides a novel route to engineer heat-resistant proteins.
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Affiliation(s)
- Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, Center for Systems Biology, Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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21
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Yasuda K, Takahashi M, Mori N. Mdm20 Modulates Actin Remodeling through the mTORC2 Pathway via Its Effect on Rictor Expression. PLoS One 2015; 10:e0142943. [PMID: 26600389 PMCID: PMC4658088 DOI: 10.1371/journal.pone.0142943] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/28/2015] [Indexed: 12/20/2022] Open
Abstract
NatB is an N-terminal acetyltransferase consisting of a catalytic Nat5 subunit and an auxiliary Mdm20 subunit. In yeast, NatB acetylates N-terminal methionines of proteins during de novo protein synthesis and also regulates actin remodeling through N-terminal acetylation of tropomyosin (Trpm), which stabilizes the actin cytoskeleton by interacting with actin. However, in mammalian cells, the biological functions of the Mdm20 and Nat5 subunits are not well understood. In the present study, we show for the first time that Mdm20-knockdown (KD), but not Nat5-KD, in HEK293 and HeLa cells suppresses not only cell growth, but also cellular motility. Although stress fibers were formed in Mdm20-KD cells, and not in control or Nat5-KD cells, the localization of Trpm did not coincide with the formation of stress fibers in Mdm20-KD cells. Notably, knockdown of Mdm20 reduced the expression of Rictor, an mTORC2 complex component, through post-translational regulation. Additionally, PKCαS657 phosphorylation, which regulates the organization of the actin cytoskeleton, was also reduced in Mdm20-KD cells. Our data also suggest that FoxO1 phosphorylation is regulated by the Mdm20-mTORC2-Akt pathway in response to serum starvation and insulin stimulation. Taken together, the present findings suggest that Mdm20 acts as a novel regulator of Rictor, thereby controlling mTORC2 activity, and leading to the activation of PKCαS657 and FoxO1.
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Affiliation(s)
- Kunihiko Yasuda
- The Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
- * E-mail: (KY); (NM)
| | - Mayumi Takahashi
- The Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Nozomu Mori
- The Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
- * E-mail: (KY); (NM)
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22
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Mughal AA, Grieg Z, Skjellegrind H, Fayzullin A, Lamkhannat M, Joel M, Ahmed MS, Murrell W, Vik-Mo EO, Langmoen IA, Stangeland B. Knockdown of NAT12/NAA30 reduces tumorigenic features of glioblastoma-initiating cells. Mol Cancer 2015; 14:160. [PMID: 26292663 PMCID: PMC4546247 DOI: 10.1186/s12943-015-0432-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 08/12/2015] [Indexed: 01/21/2023] Open
Abstract
Background Glioblastoma (GBM) is the most common primary brain malignancy and confers a dismal prognosis. GBMs harbor glioblastoma-initiating cells (GICs) that drive tumorigenesis and contribute to therapeutic resistance and tumor recurrence. Consequently, there is a strong rationale to target this cell population in order to develop new molecular therapies against GBM. Accumulating evidence indicates that Nα-terminal acetyltransferases (NATs), that are dysregulated in numerous human cancers, can serve as therapeutic targets. Methods Microarrays were used to study the expression of several NATs including NAT12/NAA30 in clinical samples and stem cell cultures. The expression of NAT12/NAA30 was analyzed using qPCR, immunolabeling and western blot. We conducted shRNA-mediated knockdown of NAT12/NAA30 gene in GICs and studied the effects on cell viability, sphere-formation and hypoxia sensitivity. Intracranial transplantation to SCID mice enabled us to investigate the effects of NAT12/NAA30 depletion in vivo. Using microarrays we identified genes and biochemical pathways whose expression was altered upon NAT12/NAA30 down-regulation. Results While decreased expression of the distal 3’UTR of NAT12/NAA30 was generally observed in GICs and GBMs, this gene was strongly up-regulated at the protein level in GBM and GICs. The increased protein levels were not caused by increased levels of the steady state mRNA but rather by other mechanisms. Also, shorter 3’UTR of NAT12/NAA30 correlated with poor survival in glioma patients. As well, we observed previously not described nuclear localization of this typically cytoplasmic protein. When compared to non-silencing controls, cells featuring NAT12/NAA30 knockdown exhibited reduced cell viability, sphere-forming ability, and mitochondrial hypoxia tolerance. Intracranial transplantation showed that knockdown of NAT12/NAA30 resulted in prolonged animal survival. Microarray analysis of the knockdown cultures showed reduced levels of HIF1α and altered expression of several other genes involved in the hypoxia response. Furthermore, NAT12/NAA30 knockdown correlated with expressional dysregulation of genes involved in the p53 pathway, ribosomal assembly and cell proliferation. Western blot analysis revealed reduction of HIF1α, phospho-MTOR(Ser2448) and higher levels of p53 and GFAP in these cultures. Conclusion NAT12/NAA30 plays an important role in growth and survival of GICs possibly by regulating hypoxia response (HIF1α), levels of p-MTOR (Ser2448) and the p53 pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0432-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Awais A Mughal
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway.
| | - Zanina Grieg
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Håvard Skjellegrind
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Artem Fayzullin
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Mustapha Lamkhannat
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Mrinal Joel
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway. .,Laboratory of Neural Development and Optical Recording (NDEVOR), Department of Physiology, Institute of Basic Medical Sciences University of Oslo, Oslo, Norway.
| | - M Shakil Ahmed
- Institute for Surgical Research, Oslo University Hospital and Center for Heart Failure Research, University of Oslo, Oslo, Norway.
| | - Wayne Murrell
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway.
| | - Einar O Vik-Mo
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Iver A Langmoen
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
| | - Biljana Stangeland
- Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway. .,SFI-CAST-Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway.
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23
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Linster E, Stephan I, Bienvenut WV, Maple-Grødem J, Myklebust LM, Huber M, Reichelt M, Sticht C, Geir Møller S, Meinnel T, Arnesen T, Giglione C, Hell R, Wirtz M. Downregulation of N-terminal acetylation triggers ABA-mediated drought responses in Arabidopsis. Nat Commun 2015; 6:7640. [PMID: 26184543 PMCID: PMC4530475 DOI: 10.1038/ncomms8640] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 05/27/2015] [Indexed: 11/08/2022] Open
Abstract
N-terminal acetylation (NTA) catalysed by N-terminal acetyltransferases (Nats) is among the most common protein modifications in eukaryotes, but its significance is still enigmatic. Here we characterize the plant NatA complex and reveal evolutionary conservation of NatA biochemical properties in higher eukaryotes and uncover specific and essential functions of NatA for development, biosynthetic pathways and stress responses in plants. We show that NTA decreases significantly after drought stress, and NatA abundance is rapidly downregulated by the phytohormone abscisic acid. Accordingly, transgenic downregulation of NatA induces the drought stress response and results in strikingly drought resistant plants. Thus, we propose that NTA by the NatA complex acts as a cellular surveillance mechanism during stress and that imprinting of the proteome by NatA is an important switch for the control of metabolism, development and cellular stress responses downstream of abscisic acid.
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
- Hartmut Hoffmann-Berling International Graduate School, University of Heidelberg, Heidelberg 69120, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
| | - Willy V. Bienvenut
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 21, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198, France
| | - Jodi Maple-Grødem
- Center for Organelle Research, University of Stavanger, Stavanger N-4036, Norway
| | - Line M. Myklebust
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Monika Huber
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
- Hartmut Hoffmann-Berling International Graduate School, University of Heidelberg, Heidelberg 69120, Germany
| | | | | | - Simon Geir Møller
- Center for Organelle Research, University of Stavanger, Stavanger N-4036, Norway
- Department of Biological Sciences, St John's University, New York, New York 11439, USA
- Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger 4068, Norway
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 21, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198, France
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
- Department of Surgery, Haukeland University Hospital, Bergen N-5021, Norway
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 21, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198, France
| | - Rüdiger Hell
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
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24
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Varland S, Osberg C, Arnesen T. N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects. Proteomics 2015; 15:2385-401. [PMID: 25914051 PMCID: PMC4692089 DOI: 10.1002/pmic.201400619] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/04/2015] [Accepted: 04/21/2015] [Indexed: 01/18/2023]
Abstract
The vast majority of eukaryotic proteins are N-terminally modified by one or more processing enzymes. Enzymes acting on the very first amino acid of a polypeptide include different peptidases, transferases, and ligases. Methionine aminopeptidases excise the initiator methionine leaving the nascent polypeptide with a newly exposed amino acid that may be further modified. N-terminal acetyl-, methyl-, myristoyl-, and palmitoyltransferases may attach an acetyl, methyl, myristoyl, or palmitoyl group, respectively, to the α-amino group of the target protein N-terminus. With the action of ubiquitin ligases, one or several ubiquitin molecules are transferred, and hence, constitute the N-terminal modification. Modifications at protein N-termini represent an important contribution to proteomic diversity and complexity, and are essential for protein regulation and cellular signaling. Consequently, dysregulation of the N-terminal modifying enzymes is implicated in human diseases. We here review the different protein N-terminal modifications occurring co- or post-translationally with emphasis on the responsible enzymes and their substrate specificities.
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Affiliation(s)
- Sylvia Varland
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Camilla Osberg
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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25
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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26
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Molecular, Cellular, and Physiological Significance of N-Terminal Acetylation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 316:267-305. [DOI: 10.1016/bs.ircmb.2015.01.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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27
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Lee KE, Ahn JY, Kim JM, Hwang CS. Synthetic lethal screen of NAA20, a catalytic subunit gene of NatB N-terminal acetylase in Saccharomyces cerevisiae. J Microbiol 2014; 52:842-8. [PMID: 25163837 DOI: 10.1007/s12275-014-3694-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023]
Abstract
The Saccharomyces cerevisiae NatB N-terminal acetylase contains a catalytic subunit Naa20 and an auxiliary subunit Naa25. To elucidate the cellular functions of the NatB, we utilized the Synthetic Genetic Array to screen for genes that are essential for cell growth in the absence of NAA20. The genome-wide synthetic lethal screen of NAA20 identified genes encoding for serine/threonine protein kinase Vps15, 1,3-beta-glucanosyltransferase Gas5, and a catabolic repression regulator Mig3. The present study suggests that the catalytic activity of the NatB N-terminal aceytase is involved in vacuolar protein sorting and cell wall maintenance.
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Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Gyeongbuk, 790-784, Republic of Korea
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28
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Zhu HY, Li CM, Wang LF, Bai H, Li YP, Yu WX, Xia DA, Liu CC. In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa). Int J Mol Sci 2014; 15:1852-64. [PMID: 24473137 PMCID: PMC3958825 DOI: 10.3390/ijms15021852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/17/2014] [Accepted: 01/18/2014] [Indexed: 11/24/2022] Open
Abstract
N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A–F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.
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Affiliation(s)
- Hang-Yong Zhu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Chun-Ming Li
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China.
| | - Li-Feng Wang
- Faculty of life Science and Technology, Mudanjiang Normal University, 191 Wenhua Street, Mudanjiang 157012, China.
| | - Hui Bai
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China.
| | - Yan-Ping Li
- Faculty of life Science and Technology, Mudanjiang Normal University, 191 Wenhua Street, Mudanjiang 157012, China.
| | - Wen-Xi Yu
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China.
| | - De-An Xia
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Chang-Cai Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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29
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Van Damme P, Støve SI, Glomnes N, Gevaert K, Arnesen T. A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant. Mol Cell Proteomics 2014; 13:2031-41. [PMID: 24408909 DOI: 10.1074/mcp.m113.035402] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) occurs on the majority of eukaryotic proteins and is catalyzed by N-terminal acetyltransferases (NATs). Nt-acetylation is increasingly recognized as a vital modification with functional implications ranging from protein degradation to protein localization. Although early genetic studies in yeast demonstrated that NAT-deletion strains displayed a variety of phenotypes, only recently, the first human genetic disorder caused by a mutation in a NAT gene was reported; boys diagnosed with the X-linked Ogden syndrome harbor a p.Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of the NatA complex, and suffer from global developmental delays and lethality during infancy. Here, we describe a Saccharomyces cerevisiae model developed by introducing the human wild-type or mutant NatA complex into yeast lacking NatA (NatA-Δ). The wild-type human NatA complex phenotypically complemented the NatA-Δ strain, whereas only a partial rescue was observed for the Ogden mutant NatA complex suggesting that hNaa10 S37P is only partially functional in vivo. Immunoprecipitation experiments revealed a reduced subunit complexation for the mutant hNatA S37P next to a reduced in vitro catalytic activity. We performed quantitative Nt-acetylome analyses on a control yeast strain (yNatA), a yeast NatA deletion strain (yNatA-Δ), a yeast NatA deletion strain expressing wild-type human NatA (hNatA), and a yeast NatA deletion strain expressing mutant human NatA (hNatA S37P). Interestingly, a generally reduced degree of Nt-acetylation was observed among a large group of NatA substrates in the yeast expressing mutant hNatA as compared with yeast expressing wild-type hNatA. Combined, these data provide strong support for the functional impairment of hNaa10 S37P in vivo and suggest that reduced Nt-acetylation of one or more target substrates contributes to the pathogenesis of the Ogden syndrome. Comparative analysis between human and yeast NatA also provided new insights into the co-evolution of the NatA complexes and their substrates. For instance, (Met-)Ala- N termini are more prevalent in the human proteome as compared with the yeast proteome, and hNatA displays a preference toward these N termini as compared with yNatA.
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Affiliation(s)
- Petra Van Damme
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium;
| | - Svein I Støve
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Nina Glomnes
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; ‖Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; and
| | - Kris Gevaert
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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30
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Yasuda K, Ohyama K, Onga K, Kakizuka A, Mori N. Mdm20 stimulates polyQ aggregation via inhibiting autophagy through Akt-Ser473 phosphorylation. PLoS One 2013; 8:e82523. [PMID: 24358196 PMCID: PMC3865000 DOI: 10.1371/journal.pone.0082523] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/24/2013] [Indexed: 01/12/2023] Open
Abstract
Mdm20 is an auxiliary subunit of the NatB complex, which includes Nat5, the catalytic subunit for protein N-terminal acetylation. The NatB complex catalyzes N-acetylation during de novo protein synthesis initiation; however, recent evidence from yeast suggests that NatB also affects post-translational modification of tropomyosin, which is involved in intracellular sorting of aggregated proteins. We hypothesized that an acetylation complex such as NatB may contribute to protein clearance and/or proteostasis in mammalian cells. Using a poly glutamine (polyQ) aggregation system, we examined whether the NatB complex or its components affect protein aggregation in rat primary cultured hippocampal neurons and HEK293 cells. The number of polyQ aggregates increased in Mdm20 over-expressing (OE) cells, but not in Nat5-OE cells. Conversely, in Mdm20 knockdown (KD) cells, but not in Nat5-KD cells, polyQ aggregation was significantly reduced. Although Mdm20 directly associates with Nat5, the overall cellular localization of the two proteins was slightly distinct, and Mdm20 apparently co-localized with the polyQ aggregates. Furthermore, in Mdm20-KD cells, a punctate appearance of LC3 was evident, suggesting the induction of autophagy. Consistent with this notion, phosphorylation of Akt, most notably at Ser473, was greatly reduced in Mdm20-KD cells. These results demonstrate that Mdm20, the so-called auxiliary subunit of the translation-coupled protein N-acetylation complex, contributes to protein clearance and/or aggregate formation by affecting the phosphorylation level of Akt indepenently from the function of Nat5.
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Affiliation(s)
- Kunihiko Yasuda
- From the Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Kyoji Ohyama
- From the Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Kazuko Onga
- From the Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Akira Kakizuka
- Laboratory of Functional Biology, Kyoto University Graduate School of Biostudies, Kyoto, Japan
| | - Nozomu Mori
- From the Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
- * E-mail:
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31
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Implications for the evolution of eukaryotic amino-terminal acetyltransferase (NAT) enzymes from the structure of an archaeal ortholog. Proc Natl Acad Sci U S A 2013; 110:14652-7. [PMID: 23959863 DOI: 10.1073/pnas.1310365110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amino-terminal acetylation is a ubiquitous modification in eukaryotes that is involved in a growing number of biological processes. There are six known eukaryotic amino-terminal acetyltransferases (NATs), which are differentiated from one another on the basis of substrate specificity. To date, two eukaryotic NATs, NatA and NatE, have been structurally characterized, of which NatA will acetylate the α-amino group of a number of nonmethionine amino-terminal residue substrates such as serine; NatE requires a substrate amino-terminal methionine residue for activity. Interestingly, these two NATs use different catalytic strategies to accomplish substrate-specific acetylation. In archaea, where this modification is less prevalent, only one NAT enzyme has been identified. Surprisingly, this enzyme is able to acetylate NatA and NatE substrates and is believed to represent an ancestral NAT variant from which the eukaryotic NAT machinery evolved. To gain insight into the evolution of NAT enzymes, we determined the X-ray crystal structure of an archaeal NAT from Sulfolobus solfataricus (ssNAT). Through the use of mutagenesis and kinetic analysis, we show that the active site of ssNAT represents a hybrid of the NatA and NatE active sites, and we highlight features of this protein that allow it to facilitate catalysis of distinct substrates through different catalytic strategies, which is a unique characteristic of this enzyme. Taken together, the structural and biochemical data presented here have implications for the evolution of eukaryotic NAT enzymes and the substrate specificities therein.
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32
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Liszczak G, Goldberg JM, Foyn H, Petersson EJ, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by the heterodimeric NatA complex. Nat Struct Mol Biol 2013; 20:1098-105. [PMID: 23912279 PMCID: PMC3766382 DOI: 10.1038/nsmb.2636] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/19/2013] [Indexed: 12/23/2022]
Abstract
Amino-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this co-translational modification, the heterodimeric NatA complex harbors the most diversity for substrate selection and modifies the majority of all amino-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100 kDa holo-NatA complex from Schizosaccharomyces pombe in the absence and presence of a bisubstrate peptide-CoA conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 TPR motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.
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Affiliation(s)
- Glen Liszczak
- 1] Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania, USA. [2] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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33
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McDowell GS, Philpott A. Non-canonical ubiquitylation: mechanisms and consequences. Int J Biochem Cell Biol 2013; 45:1833-42. [PMID: 23732108 DOI: 10.1016/j.biocel.2013.05.026] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/10/2013] [Accepted: 05/22/2013] [Indexed: 01/04/2023]
Abstract
Post-translational protein modifications initiate, regulate, propagate and terminate a wide variety of processes in cells, and in particular, ubiquitylation targets substrate proteins for degradation, subcellular translocation, cell signaling and multiple other cellular events. Modification of substrate proteins is widely observed to occur via covalent linkages of ubiquitin to the amine groups of lysine side-chains. However, in recent years several new modes of ubiquitin chain attachment have emerged. For instance, covalent modification of non-lysine sites in substrate proteins is theoretically possible according to basic chemical principles underlying the ubiquitylation process, and evidence is building that sites such as the N-terminal amine group of a protein, the hydroxyl group of serine and threonine residues and even the thiol groups of cysteine residues are all employed as sites of ubiquitylation. However, the potential importance of this "non-canonical ubiquitylation" of substrate proteins on sites other than lysine residues has been largely overlooked. This review aims to highlight the unusual features of the process of non-canonical ubiquitylation and the consequences of these events on the activity and fate of a protein.
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Affiliation(s)
- Gary S McDowell
- Department of Oncology, University of Cambridge, Hutchison/Medical Research Council (MRC) Research Centre, Cambridge, UK
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34
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Mathiasen DP, Gallina I, Germann SM, Hamou W, Eléouët M, Thodberg S, Eckert-Boulet N, Game J, Lisby M. Physical mapping and cloning of RAD56. Gene X 2013; 519:182-6. [DOI: 10.1016/j.gene.2013.01.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/16/2022] Open
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35
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Liu CC, Zhu HY, Dong XM, Ning DL, Wang HX, Li WH, Yang CP, Wang BC. Identification and analysis of the acetylated status of poplar proteins reveals analogous N-terminal protein processing mechanisms with other eukaryotes. PLoS One 2013; 8:e58681. [PMID: 23536812 PMCID: PMC3594182 DOI: 10.1371/journal.pone.0058681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/05/2013] [Indexed: 11/22/2022] Open
Abstract
Background The N-terminal protein processing mechanism (NPM) including N-terminal Met excision (NME) and N-terminal acetylation (Nα-acetylation) represents a common protein co-translational process of some eukaryotes. However, this NPM occurred in woody plants yet remains unknown. Methodology/Principal Findings To reveal the NPM in poplar, we investigated the Nα-acetylation status of poplar proteins during dormancy by combining tandem mass spectrometry with TiO2 enrichment of acetylated peptides. We identified 58 N-terminally acetylated (Nα-acetylated) proteins. Most proteins (47, >81%) are subjected to Nα-acetylation following the N-terminal removal of Met, indicating that Nα-acetylation and NME represent a common NPM of poplar proteins. Furthermore, we confirm that poplar shares the analogous NME and Nα-acetylation (NPM) to other eukaryotes according to analysis of N-terminal features of these acetylated proteins combined with genome-wide identification of the involving methionine aminopeptidases (MAPs) and N-terminal acetyltransferase (Nat) enzymes in poplar. The Nα-acetylated reactions and the involving enzymes of these poplar proteins are also identified based on those of yeast and human, as well as the subcellular location information of these poplar proteins. Conclusions/Significance This study represents the first extensive investigation of Nα-acetylation events in woody plants, the results of which will provide useful resources for future unraveling the regulatory mechanisms of Nα-acetylation of proteins in poplar.
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Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- Laboratory for Chemical Defense and Microscale Analysis, Hubei Nanxing General Chemical Factory, Zhijiang, Hubei, China
| | - Hang-Yong Zhu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- Bureau of Garden and Park, Qitaihe, Heilongjiang, China
| | - Xiu-Mei Dong
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
| | - De-Li Ning
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hong-Xia Wang
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, Beijing, China
| | - Wei-Hua Li
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, Beijing, China
| | - Chuan-Ping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- * E-mail: (C-PY); (B-CW)
| | - Bai-Chen Wang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (C-PY); (B-CW)
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Drosophila Psidin regulates olfactory neuron number and axon targeting through two distinct molecular mechanisms. J Neurosci 2013; 32:16080-94. [PMID: 23152593 DOI: 10.1523/jneurosci.3116-12.2012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The formation of neuronal circuits is a key process of development, laying foundations for behavior. The cellular mechanisms regulating circuit development are not fully understood. Here, we reveal Psidin as an intracellular regulator of Drosophila olfactory system formation. We show that Psidin is required in several classes of olfactory receptor neurons (ORNs) for survival and subsequently for axon guidance. During axon guidance, Psidin functions as an actin regulator and antagonist of Tropomyosin. Accordingly, Psidin-deficient primary neurons in culture display growth cones with significantly smaller lamellipodia. This lamellipodial phenotype, as well as the mistargeting defects in vivo, is suppressed by parallel removal of Tropomyosin. In contrast, Psidin functions as the noncatalytic subunit of the N-acetyltransferase complex B (NatB) to maintain the number of ORNs. Psidin physically binds the catalytic NatB subunit CG14222 (dNAA20) and functionally interacts with it in vivo. We define the dNAA20 interaction domain within Psidin and identify a conserved serine as a candidate for phosphorylation-mediated regulation of NatB complex formation. A phosphomimetic mutation of this serine showed severely reduced binding to dNAA20 in vitro. In vivo, it fully rescued the targeting defect but not the reduction in neuron numbers. In addition, we show that a different amino acid point mutation shows exactly the opposite effect by rescuing only the cell number but not the axon targeting defect. Together, our data suggest that Psidin plays two independent developmental roles via the acquisition of separate signaling pathways, both of which contribute to the formation of olfactory circuits.
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37
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Structural characterization of a eukaryotic chaperone--the ribosome-associated complex. Nat Struct Mol Biol 2012. [PMID: 23202586 DOI: 10.1038/nsmb.2447] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ribosome-associated chaperones act in early folding events during protein synthesis. Structural information is available for prokaryotic chaperones (such as trigger factor), but structural understanding of these processes in eukaryotes lags far behind. Here we present structural analyses of the eukaryotic ribosome-associated complex (RAC) from Saccharomyces cerevisiae and Chaetomium thermophilum, consisting of heat-shock protein 70 (Hsp70) Ssz1 and the Hsp40 Zuo1. RAC is an elongated complex that crouches over the ribosomal tunnel exit and seems to be stabilized in a distinct conformation by expansion segment ES27. A unique α-helical domain in Zuo1 mediates ribosome interaction of RAC near the ribosomal proteins L22e and L31e and ribosomal RNA helix H59. The crystal structure of the Ssz1 ATPase domain bound to ATP-Mg²⁺ explains its catalytic inactivity and suggests that Ssz1 may act before the RAC-associated chaperone Ssb. Our study offers insights into the interplay between RAC, the ER membrane-integrated Hsp40-type protein ERj1 and the signal-recognition particle.
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Permyakov SE, Vologzhannikova AA, Emelyanenko VI, Knyazeva EL, Kazakov AS, Lapteva YS, Permyakova ME, Zhadan AP, Permyakov EA. The impact of alpha-N-acetylation on structural and functional status of parvalbumin. Cell Calcium 2012; 52:366-76. [DOI: 10.1016/j.ceca.2012.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/30/2012] [Accepted: 06/01/2012] [Indexed: 01/09/2023]
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39
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Voordeckers K, De Maeyer D, van der Zande E, Vinces MD, Meert W, Cloots L, Ryan O, Marchal K, Verstrepen KJ. Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology. Mol Microbiol 2012; 86:225-39. [PMID: 22882838 PMCID: PMC3470922 DOI: 10.1111/j.1365-2958.2012.08192.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2012] [Indexed: 01/08/2023]
Abstract
When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much attention recently. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signalling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, with one notable example being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters for fine-tuning FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive look at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.
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Affiliation(s)
- Karin Voordeckers
- Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001, Leuven, Belgium
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40
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Linkage analysis of extended high-risk pedigrees replicates a cutaneous malignant melanoma predisposition locus on chromosome 9q21. J Invest Dermatol 2012; 133:128-34. [PMID: 22951724 PMCID: PMC3535071 DOI: 10.1038/jid.2012.271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Three predisposition genes have been identified for cutaneous malignant melanoma (CMM), but they account for only about 25% of melanoma clusters/pedigrees. Linkage analyses of melanoma pedigrees from many countries have failed to identify significant linkage evidence for the remaining predisposition genes that must exist. The Utah linkage analysis approach of using singly informative extended high-risk pedigrees combined with high-density SNP markers has successfully identified significant linkage evidence for two regions. This first genome-wide linkage analysis of the extended Utah high-risk CMM pedigrees provides confirmation of linkage for a chromosome 9q region previously reported in Danish pedigrees. This report confirms that linkage analysis for common disorders can be successful in analysis of high-density markers in sets of singly informative high-risk pedigrees.
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41
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N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB. Proc Natl Acad Sci U S A 2012; 109:12449-54. [PMID: 22814378 DOI: 10.1073/pnas.1210303109] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Protein N-terminal acetylation (Nt-acetylation) is an important mediator of protein function, stability, sorting, and localization. Although the responsible enzymes are thought to be fairly well characterized, the lack of identified in vivo substrates, the occurrence of Nt-acetylation substrates displaying yet uncharacterized N-terminal acetyltransferase (NAT) specificities, and emerging evidence of posttranslational Nt-acetylation, necessitate the use of genetic models and quantitative proteomics. NatB, which targets Met-Glu-, Met-Asp-, and Met-Asn-starting protein N termini, is presumed to Nt-acetylate 15% of all yeast and 18% of all human proteins. We here report on the evolutionary traits of NatB from yeast to human and demonstrate that ectopically expressed hNatB in a yNatB-Δ yeast strain partially complements the natB-Δ phenotypes and partially restores the yNatB Nt-acetylome. Overall, combining quantitative N-terminomics with yeast studies and knockdown of hNatB in human cell lines, led to the unambiguous identification of 180 human and 110 yeast NatB substrates. Interestingly, these substrates included Met-Gln- N-termini, which are thus now classified as in vivo NatB substrates. We also demonstrate the requirement of hNatB activity for maintaining the structure and function of actomyosin fibers and for proper cellular migration. In addition, expression of tropomyosin-1 restored the altered focal adhesions and cellular migration defects observed in hNatB-depleted HeLa cells, indicative for the conserved link between NatB, tropomyosin, and actin cable function from yeast to human.
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42
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Birke H, Müller SJ, Rother M, Zimmer AD, Hoernstein SNW, Wesenberg D, Wirtz M, Krauss GJ, Reski R, Hell R. The relevance of compartmentation for cysteine synthesis in phototrophic organisms. PROTOPLASMA 2012; 249 Suppl 2:S147-55. [PMID: 22543690 DOI: 10.1007/s00709-012-0411-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/10/2012] [Indexed: 05/18/2023]
Abstract
In the vascular plant Arabidopsis thaliana, synthesis of cysteine and its precursors O-acetylserine and sulfide is distributed between the cytosol, chloroplasts, and mitochondria. This compartmentation contributes to regulation of cysteine synthesis. In contrast to Arabidopsis, cysteine synthesis is exclusively restricted to chloroplasts in the unicellular green alga Chlamydomonas reinhardtii. Thus, the question arises, whether specification of compartmentation was driven by multicellularity and specified organs and tissues. The moss Physcomitrella patens colonizes land but is still characterized by a simple morphology compared to vascular plants. It was therefore used as model organism to study evolution of compartmented cysteine synthesis. The presence of O-acetylserine(thiol)lyase (OAS-TL) proteins, which catalyze the final step of cysteine synthesis, in different compartments was applied as criterion. Purification and characterization of native OAS-TL proteins demonstrated the presence of five OAS-TL protein species encoded by two genes in Physcomitrella. At least one of the gene products is dual targeted to plastids and cytosol, as shown by combination of GFP fusion localization studies, purification of chloroplasts, and identification of N termini from native proteins. The bulk of OAS-TL protein is targeted to plastids, whereas there is no evidence for a mitochondrial OAS-TL isoform and only a minor part of OAS-TL protein is localized in the cytosol. This demonstrates that subcellular diversification of cysteine synthesis is already initialized in Physcomitrella but appears to gain relevance later during evolution of vascular plants.
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Affiliation(s)
- Hannah Birke
- Centre for Organismal Studies Heidelberg, Department Plant Molecular Biology, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
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Starheim KK, Gevaert K, Arnesen T. Protein N-terminal acetyltransferases: when the start matters. Trends Biochem Sci 2012; 37:152-61. [PMID: 22405572 DOI: 10.1016/j.tibs.2012.02.003] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 01/02/2023]
Abstract
The majority of eukaryotic proteins are subjected to N-terminal acetylation (Nt-acetylation), catalysed by N-terminal acetyltransferases (NATs). Recently, the structure of an NAT-peptide complex was determined, and detailed proteome-wide Nt-acetylation patterns were revealed. Furthermore, Nt-acetylation just emerged as a multifunctional regulator, acting as a protein degradation signal, an inhibitor of endoplasmic reticulum (ER) translocation, and a mediator of protein complex formation. Nt-acetylation is regulated by acetyl-coenzyme A (Ac-CoA) levels, and thereby links metabolic cell states to cell death. The essentiality of NATs in humans is stressed by the recent discovery of a human hereditary lethal disease caused by a mutation in an NAT gene. Here, we discuss how these recent findings shed light on NATs as major protein regulators and key cellular players.
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44
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Matsuo T, Iida T, Ishiura M. N-terminal acetyltransferase 3 gene is essential for robust circadian rhythm of bioluminescence reporter in Chlamydomonas reinhardtii. Biochem Biophys Res Commun 2012; 418:342-6. [PMID: 22266323 DOI: 10.1016/j.bbrc.2012.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 01/06/2012] [Indexed: 11/19/2022]
Abstract
Chlamydomonas reinhardtii is a model species of algae for studies on the circadian clock. Previously, we isolated a series of mutants showing defects in the circadian rhythm of a luciferase reporter introduced into the chloroplast genome, and identified the genes responsible for the defective circadian rhythm. However, we were unable to identify the gene responsible for the defective circadian rhythm of the rhythm of chloroplast 97 (roc97) mutant because of a large genomic deletion. Here, we identified the gene responsible for the roc97 mutation through a genetic complementation study. This gene encodes a protein that is homologous to the subunit of N-terminal acetyltransferase (NAT) which catalyzes N-terminal acetylation of proteins. Our results provide the first example of involvement of the protein N-terminal acetyltransferase in the circadian rhythm.
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Affiliation(s)
- Takuya Matsuo
- Center for Gene Research, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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45
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Ohyama K, Yasuda K, Onga K, Kakizuka A, Mori N. Spatio-temporal expression pattern of the NatB complex, Nat5/Mdm20 in the developing mouse brain: implications for co-operative versus non-co-operative actions of Mdm20 and Nat5. Gene Expr Patterns 2011; 12:36-45. [PMID: 22101279 DOI: 10.1016/j.gep.2011.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 01/08/2023]
Abstract
The NatB complex, Nat5/Mdm20 acetyltransferase mediates N-acetylation to control cell cycle progression and actin dynamics in yeast. As yet, little is known about the expression pattern of Mdm20 and Nat5 in multi-cellular organisms. Here we show that Mdm20 is highly expressed in mouse embryonic brain. At E11.5, Mdm20 was widely expressed in both neural progenitors and early differentiating neurons, whereas Nat5 was expressed in Sox1/3+/Mdm20+ neural progenitors. By E14.5, both Mdm20 and Nat5 were downregulated in most ventricular zone neural progenitors, whereas both proteins were found in differentiating neurons and co-expression was maintained at E18.5 in derivatives of these cells, such as midbrain dopaminergic (DA) neurons and septal neurons. These data suggest that Nat5/Mdm20 complex-mediated acetylation may play a role in the proliferation and differentiation of neural progenitors. Intriguingly, our data also showed that Mdm20 is not always co-expressed with Nat5 in all differentiated neurons, for example deep cerebellar neurons. Moreover, detailed examination of the subcellular localization of Mdm20 and Nat5 in cultured Nat5+/Mdm20+ midbrain DA neurons revealed that Mdm20 is also not necessarily co-localized with Nat5 within neurons. Given that Nat5 is only a known member of Nat family protein that interacts with Mdm20, our data imply that Mdm20 may function either with an unidentified Nat protein partner(s) or possibly in a Nat-independent manner.
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Affiliation(s)
- Kyoji Ohyama
- Department of Anatomy and Neurobiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
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46
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Scott DC, Monda JK, Bennett EJ, Harper JW, Schulman BA. N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex. Science 2011; 334:674-8. [PMID: 21940857 PMCID: PMC3214010 DOI: 10.1126/science.1209307] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although many eukaryotic proteins are amino (N)-terminally acetylated, structural mechanisms by which N-terminal acetylation mediates protein interactions are largely unknown. Here, we found that N-terminal acetylation of the E2 enzyme, Ubc12, dictates distinctive E3-dependent ligation of the ubiquitin-like protein Nedd8 to Cul1. Structural, biochemical, biophysical, and genetic analyses revealed how complete burial of Ubc12's N-acetyl-methionine in a hydrophobic pocket in the E3, Dcn1, promotes cullin neddylation. The results suggest that the N-terminal acetyl both directs Ubc12's interactions with Dcn1 and prevents repulsion of a charged N terminus. Our data provide a link between acetylation and ubiquitin-like protein conjugation and define a mechanism for N-terminal acetylation-dependent recognition.
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Affiliation(s)
- Daniel C Scott
- Structural Biology Department, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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47
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Liszczak G, Arnesen T, Marmorstein R. Structure of a ternary Naa50p (NAT5/SAN) N-terminal acetyltransferase complex reveals the molecular basis for substrate-specific acetylation. J Biol Chem 2011; 286:37002-10. [PMID: 21900231 PMCID: PMC3196119 DOI: 10.1074/jbc.m111.282863] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/26/2011] [Indexed: 01/28/2023] Open
Abstract
The co-translational modification of N-terminal acetylation is ubiquitous among eukaryotes and has been reported to have a wide range of biological effects. The human N-terminal acetyltransferase (NAT) Naa50p (NAT5/SAN) acetylates the α-amino group of proteins containing an N-terminal methionine residue and is essential for proper sister chromatid cohesion and chromosome condensation. The elevated activity of NATs has also been correlated with cancer, making these enzymes attractive therapeutic targets. We report the x-ray crystal structure of Naa50p bound to a native substrate peptide fragment and CoA. We found that the peptide backbone of the substrate is anchored to the protein through a series of backbone hydrogen bonds with the first methionine residue specified through multiple van der Waals contacts, together creating an α-amino methionine-specific pocket. We also employed structure-based mutagenesis; the results support the importance of the α-amino methionine-specific pocket of Naa50p and are consistent with the proposal that conserved histidine and tyrosine residues play important catalytic roles. Superposition of the ternary Naa50p complex with the peptide-bound Gcn5 histone acetyltransferase revealed that the two enzymes share a Gcn5-related N-acetyltransferase fold but differ in their respective substrate-binding grooves such that Naa50p can accommodate only an α-amino substrate and not a side chain lysine substrate that is acetylated by lysine acetyltransferase enzymes such as Gcn5. The structure of the ternary Naa50p complex also provides the first molecular scaffold for the design of NAT-specific small molecule inhibitors with possible therapeutic applications.
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Affiliation(s)
- Glen Liszczak
- From The Wistar Institute and
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Thomas Arnesen
- the Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway, and
- the Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ronen Marmorstein
- From The Wistar Institute and
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival. Cell 2011; 146:607-20. [PMID: 21854985 DOI: 10.1016/j.cell.2011.06.050] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 07/06/2010] [Accepted: 06/23/2011] [Indexed: 01/10/2023]
Abstract
Previous experiments suggest a connection between the N-alpha-acetylation of proteins and sensitivity of cells to apoptotic signals. Here, we describe a biochemical assay to detect the acetylation status of proteins and demonstrate that protein N-alpha-acetylation is regulated by the availability of acetyl-CoA. Because the antiapoptotic protein Bcl-xL is known to influence mitochondrial metabolism, we reasoned that Bcl-xL may provide a link between protein N-alpha-acetylation and apoptosis. Indeed, Bcl-xL overexpression leads to a reduction in levels of acetyl-CoA and N-alpha-acetylated proteins in the cell. This effect is independent of Bax and Bak, the known binding partners of Bcl-xL. Increasing cellular levels of acetyl-CoA by addition of acetate or citrate restores protein N-alpha-acetylation in Bcl-xL-expressing cells and confers sensitivity to apoptotic stimuli. We propose that acetyl-CoA serves as a signaling molecule that couples apoptotic sensitivity to metabolism by regulating protein N-alpha-acetylation.
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49
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Wang Y, Mijares M, Gall MD, Turan T, Javier A, Bornemann DJ, Manage K, Warrior R. Drosophila variable nurse cells encodes arrest defective 1 (ARD1), the catalytic subunit of the major N-terminal acetyltransferase complex. Dev Dyn 2011; 239:2813-27. [PMID: 20882681 DOI: 10.1002/dvdy.22418] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Mutations in the Drosophila variable nurse cells (vnc) gene result in female sterility and oogenesis defects, including egg chambers with too many or too few nurse cells. We show that vnc corresponds to Arrest Defective1 (Ard1) and encodes the catalytic subunit of NatA, the major N-terminal acetyl-transferase complex. While N-terminal acetylation is one of the most prevalent covalent protein modifications in eukaryotes, analysis of its role in development has been challenging since mutants that compromise NatA activity have not been described in any multicellular animal. Our data show that reduced ARD1 levels result in pleiotropic oogenesis defects including abnormal cyst encapsulation, desynchronized cystocyte division, disrupted nurse cell chromosome dispersion, and abnormal chorion patterning, consistent with the wide range of predicted NatA substrates. Furthermore, we find that loss of Ard1 affects cell survival/proliferation and is lethal for the animal, providing the first demonstration that this modification is essential in higher eukaryotes.
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Affiliation(s)
- Ying Wang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA
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50
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Mischerikow N, Heck AJR. Targeted large-scale analysis of protein acetylation. Proteomics 2011; 11:571-89. [DOI: 10.1002/pmic.201000397] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/10/2010] [Accepted: 09/27/2010] [Indexed: 11/06/2022]
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