Journal Article

The tubulin database: Linking mutations, modifications, ligands and local interactions

Nag, Hindol, Tomar, Ishaan, Mushayeed, Faliha, Day, Shania Deon, Truong, Danny, Haro-Ramirez, Nancy, Abbaali, Izra, Shah, Priya, Pham, Catherine, Manel-Romero, Carolina, Ganesh, Bhargavi, Isles, Juliet, Morrissette, Naomi S.

2023

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Algorithms / Amino acid substitution / Amino acids / Amino Acids - metabolism / Analysis / Biochemistry / Composition / Cytoskeleton - metabolism / Datasets / Doublecortin protein / Dynein / Filaments / Genes / Insects / Internet resources / Isotypes / Ligands / Medical research / Medicine, Experimental / Microtubules / Microtubules - metabolism / Missense mutation / Mutation / Numbering schemes / Organisms / Phenotypes / Post-translation / Proteins / Reptiles & amphibians / Structure / Tubulin / Tubulin - metabolism / Tubulins