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Abbaali I, Truong D, Day SD, Mushayeed F, Ganesh B, Haro-Ramirez N, Isles J, Nag H, Pham C, Shah P, Tomar I, Manel-Romero C, Morrissette NS. The tubulin database: Linking mutations, modifications, ligands and local interactions. PLoS One 2023; 18:e0295279. [PMID: 38064432 PMCID: PMC10707541 DOI: 10.1371/journal.pone.0295279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Microtubules are polymeric filaments, constructed of α-β tubulin heterodimers that underlie critical subcellular structures in eukaryotic organisms. Four homologous proteins (γ-, δ-, ε- and ζ-tubulin) additionally contribute to specialized microtubule functions. Although there is an immense volume of publicly available data pertaining to tubulins, it is difficult to assimilate all potentially relevant information across diverse organisms, isotypes, and categories of data. We previously assembled an extensive web-based catalogue of published missense mutations to tubulins with >1,500 entries that each document a specific substitution to a discrete tubulin, the species where the mutation was described and the associated phenotype with hyperlinks to the amino acid sequence and citation(s) for research. This report describes a significant update and expansion of our online resource (TubulinDB.bio.uci.edu) to nearly 18,000 entries. It now encompasses a cross-referenced catalog of post-translational modifications (PTMs) to tubulin drawn from public datasets, primary literature, and predictive algorithms. In addition, tubulin protein structures were used to define local interactions with bound ligands (GTP, GDP and diverse microtubule-targeting agents) and amino acids at the intradimer interface, within the microtubule lattice and with associated proteins. To effectively cross-reference these datasets, we established a universal tubulin numbering system to map entries into a common framework that accommodates specific insertions and deletions to tubulins. Indexing and cross-referencing permitted us to discern previously unappreciated patterns. We describe previously unlinked observations of loss of PTM sites in the context of cancer cells and tubulinopathies. Similarly, we expanded the set of clinical substitutions that may compromise MAP or microtubule-motor interactions by collecting tubulin missense mutations that alter amino acids at the interface with dynein and doublecortin. By expanding the database as a curated resource, we hope to relate model organism data to clinical findings of pathogenic tubulin variants. Ultimately, we aim to aid researchers in hypothesis generation and design of studies to dissect tubulin function.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Shania Deon Day
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Faliha Mushayeed
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Bhargavi Ganesh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Nancy Haro-Ramirez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Juliet Isles
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Hindol Nag
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Catherine Pham
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Priya Shah
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Ishaan Tomar
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Carolina Manel-Romero
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Naomi S. Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
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Palma-Barqueros V, Bury L, Kunishima S, Lozano ML, Rodríguez-Alen A, Revilla N, Bohdan N, Padilla J, Fernández-Pérez MP, de la Morena-Barrio ME, Marín-Quiles A, Benito R, López-Fernández MF, Marcellini S, Zamora-Cánovas A, Vicente V, Martínez C, Gresele P, Bastida JM, Rivera J. Expanding the genetic spectrum of TUBB1-related thrombocytopenia. Blood Adv 2021; 5:5453-5467. [PMID: 34516618 PMCID: PMC8714720 DOI: 10.1182/bloodadvances.2020004057] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/20/2021] [Indexed: 11/20/2022] Open
Abstract
β1-Tubulin plays a major role in proplatelet formation and platelet shape maintenance, and pathogenic variants in TUBB1 lead to thrombocytopenia and platelet anisocytosis (TUBB1-RT). To date, the reported number of pedigrees with TUBB1-RT and of rare TUBB1 variants with experimental demonstration of pathogenicity is limited. Here, we report 9 unrelated families presenting with thrombocytopenia carrying 6 β1-tubulin variants, p.Cys12LeufsTer12, p.Thr107Pro, p.Gln423*, p.Arg359Trp, p.Gly109Glu, and p.Gly269Asp, the last of which novel. Segregation studies showed incomplete penetrance of these variants for platelet traits. Indeed, most carriers showed macrothrombocytopenia, some only increased platelet size, and a minority had no abnormalities. Moreover, only homozygous carriers of the p.Gly109Glu variant displayed macrothrombocytopenia, highlighting the importance of allele burden in the phenotypic expression of TUBB1-RT. The p.Arg359Trp, p.Gly269Asp, and p.Gly109Glu variants deranged β1-tubulin incorporation into the microtubular marginal ring in platelets but had a negligible effect on platelet activation, secretion, or spreading, suggesting that β1-tubulin is dispensable for these processes. Transfection of TUBB1 missense variants in CHO cells altered β1-tubulin incorporation into the microtubular network. In addition, TUBB1 variants markedly impaired proplatelet formation from peripheral blood CD34+ cell-derived megakaryocytes. Our study, using in vitro modeling, molecular characterization, and clinical investigations provides a deeper insight into the pathogenicity of rare TUBB1 variants. These novel data expand the genetic spectrum of TUBB1-RT and highlight a remarkable heterogeneity in its clinical presentation, indicating that allelic burden or combination with other genetic or environmental factors modulate the phenotypic impact of rare TUBB1 variants.
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Affiliation(s)
- Verónica Palma-Barqueros
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - Loredana Bury
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Shinji Kunishima
- Department of Medical Technology, Gifu University of Medical Science, Seki, Japan
| | - María Luisa Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - Augustín Rodríguez-Alen
- Servicio de Hematología y Hemoterapia, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Toledo, Spain
| | - Nuria Revilla
- Servicio de Hematología, Hospital Universitario Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Natalia Bohdan
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - José Padilla
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - María P. Fernández-Pérez
- Servicio de Hematología, Hospital Universitario Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - Ana Marín-Quiles
- Instituto de Investigación Biomédica de Salamanca, Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, Universidad de Salamanca-Consejo Superior de Investigaciones Científicas
| | - Rocío Benito
- Instituto de Investigación Biomédica de Salamanca, Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, Universidad de Salamanca-Consejo Superior de Investigaciones Científicas
| | | | | | - Ana Zamora-Cánovas
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - Vicente Vicente
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
| | - Constantino Martínez
- Servicio de Hematología, Hospital Universitario Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Paolo Gresele
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - José M. Bastida
- Departamento de Hematología, IBSAL-Hospital Universitario de Salamanca, Salamanca, Spain
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Centro de Investigacién Biomódica en Red de Enfermedades Raras-U765, Murcia, Spain
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