3
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Bondarchuk TV, Shalak VF, Lozhko DM, Fatalska A, Szczepanowski R, Liudkovska V, Tsuvariev O, Dadlez M, El'skaya A, Negrutskii B. Quaternary organization of the human eEF1B complex reveals unique multi-GEF domain assembly. Nucleic Acids Res 2022; 50:9490-9504. [PMID: 35971611 PMCID: PMC9458455 DOI: 10.1093/nar/gkac685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/12/2022] [Accepted: 07/31/2022] [Indexed: 12/24/2022] Open
Abstract
Protein synthesis in eukaryotic cell is spatially and structurally compartmentalized that ensures high efficiency of this process. One of the distinctive features of higher eukaryotes is the existence of stable multi-protein complexes of aminoacyl-tRNA synthetases and translation elongation factors. Here, we report a quaternary organization of the human guanine-nucleotide exchange factor (GEF) complex, eEF1B, comprising α, β and γ subunits that specifically associate into a heterotrimeric form eEF1B(αβγ)3. As both the eEF1Bα and eEF1Bβ proteins have structurally conserved GEF domains, their total number within the complex is equal to six. Such, so far, unique structural assembly of the guanine-nucleotide exchange factors within a stable complex may be considered as a 'GEF hub' that ensures efficient maintenance of the translationally active GTP-bound conformation of eEF1A in higher eukaryotes.
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Affiliation(s)
- Tetiana V Bondarchuk
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Vyacheslav F Shalak
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Dmytro M Lozhko
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Agnieszka Fatalska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego 5a, 02-109 Warsaw, Poland
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Vladyslava Liudkovska
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Oleksandr Yu Tsuvariev
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Akademik Glushkov Ave. 4-g, 03022 Kyiv, Ukraine
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego 5a, 02-109 Warsaw, Poland
| | - Anna V El'skaya
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Boris S Negrutskii
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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6
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Carvill GL, Helbig KL, Myers CT, Scala M, Huether R, Lewis S, Kruer TN, Guida BS, Bakhtiari S, Sebe J, Tang S, Stickney H, Oktay SU, Bhandiwad AA, Ramsey K, Narayanan V, Feyma T, Rohena LO, Accogli A, Severino M, Hollingsworth G, Gill D, Depienne C, Nava C, Sadleir LG, Caruso PA, Lin AE, Jansen FE, Koeleman B, Brilstra E, Willemsen MH, Kleefstra T, Sa J, Mathieu ML, Perrin L, Lesca G, Striano P, Casari G, Scheffer IE, Raible D, Sattlegger E, Capra V, Padilla-Lopez S, Mefford HC, Kruer MC. Damaging de novo missense variants in EEF1A2 lead to a developmental and degenerative epileptic-dyskinetic encephalopathy. Hum Mutat 2020; 41:1263-1279. [PMID: 32196822 DOI: 10.1002/humu.24015] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
Abstract
Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.
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Affiliation(s)
- Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, Illinois
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Marcello Scala
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Robert Huether
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Sara Lewis
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Tyler N Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Brandon S Guida
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Joy Sebe
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Heather Stickney
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sehribani Ulusoy Oktay
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Ashwin A Bhandiwad
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Timothy Feyma
- Department of Neurology, Gillette Children's Specialty Healthcare, St. Paul, Minnesota
| | - Luis O Rohena
- Department of Pediatrics, Division of Genetics, San Antonio Military Medical Center, San Antonio, Texas.,Department of Pediatrics, Long School of Medicine, University of Texas, San Antonio, Texas
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy.,Medical Genetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Mariasavina Severino
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Georgina Hollingsworth
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - Deepak Gill
- Ty Nelson Department of Neurology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Christel Depienne
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Caroline Nava
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington South, New Zealand
| | - Paul A Caruso
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Angela E Lin
- Medical Genetics, Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, Massachusetts
| | - Floor E Jansen
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Bobby Koeleman
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Eva Brilstra
- Department of Genetics, Utrecht University, Utrecht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joaquim Sa
- Serviço de Genética Médica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Marie-Laure Mathieu
- Neuropaediatrics Department, Femme Mère Enfant Hospital, Lyon, France.,Claude Bernard Lyon 1 University, Lyon, France
| | - Laurine Perrin
- Department of Paediatric Physical Medicine and Rehabilitation, CHU Saint-Etienne, Hôpital Bellevue, Saint-Étienne, France
| | - Gaetan Lesca
- CRNL Inserm U1028-CNRS UMR5292-Claude Bernard University Lyon 1, Lyon, France.,Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Pasquale Striano
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Giorgio Casari
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Ingrid E Scheffer
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - David Raible
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Evelyn Sattlegger
- School of Natural & Computational Sciences, Massey University, Auckland, New Zealand
| | - Valeria Capra
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Michael C Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
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7
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Tshabalala TN, Tomescu MS, Prior A, Balakrishnan V, Sayed Y, Dirr HW, Achilonu I. Energetics of Glutathione Binding to Human Eukaryotic Elongation Factor 1 Gamma: Isothermal Titration Calorimetry and Molecular Dynamics Studies. Protein J 2016; 35:448-458. [PMID: 27844275 DOI: 10.1007/s10930-016-9688-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The energetics of ligand binding to human eukaryotic elongation factor 1 gamma (heEF1γ) was investigated using reduced glutathione (GSH), oxidised glutathione (GSSG), glutathione sulfonate and S-hexylglutathione as ligands. The experiments were conducted using isothermal titration calorimetry, and the findings were supported using computational studies. The data show that the binding of these ligands to heEF1γ is enthalpically favourable and entropically driven (except for the binding of GSSG). The full length heEF1γ binds GSSG with lower affinity (K d = 115 μM), with more hydrogen-bond contacts (ΔH = -73.8 kJ/mol) and unfavourable entropy (-TΔS = 51.7 kJ/mol) compared to the glutathione transferase-like N-terminus domain of heEF1γ, which did not show preference to any specific ligand. Computational free binding energy calculations from the 10 ligand poses show that GSSG and GSH consistently bind heEF1γ, and that both ligands bind at the same site with a folded bioactive conformation. This study reveals the possibility that heEF1γ is a glutathione-binding protein.
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Affiliation(s)
- Thabiso N Tshabalala
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Mihai-Silviu Tomescu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Allan Prior
- School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Vijayakumar Balakrishnan
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Heini W Dirr
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2050, South Africa.
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