Molecular Evidence for β-tubulin Neofunctionalization in Retaria (Foraminifera and Radiolarians)

Foraminifera and radiolarians are closely related amoeboid protists (i.e., retarians) often characterized by their shells and pseudopodia. Previous studies hypothesized that the unusual Type 2 beta-tubulin (beta 2) is critically involved in forming helical filaments (HFs), a unique microtubule (MT) assembly/disassembly intermediate found in foraminiferan reticulopodia. Such noncanonical beta-tubulin sequences have also been found in two radiolarian species and appear to be closely related to the foraminiferan beta 2. In this study, we report 119 new beta-tubulin transcript sequences from six foraminiferans, four radiolarians, and a related non-retarian species. We found that foraminiferan and radiolarian beta 2-tubulins share some of the unusual substitutions in the structurally essential and usually conserved domains. In the beta-tubulin phylogeny, retarian beta 2-tubulin forms a monophyletic clade, well separated from the canonical beta-tubulin (beta 1) ubiquitous in eukaryotes. Furthermore, we found that foraminiferan and radiolarian beta 2-tubulin lineages were under positive selection, and used homology models for foraminiferan alpha- and beta-tubulin hexamers to understand the structural effect of the positively selected substitutions. We suggest that the positively selected substitutions play key roles in the transition of MT to HF by altering the lateral and longitudinal interactions between alpha- and beta-tubulin heterodimers. Our results indicate that the unusual beta 2-tubulin is a molecular synapomorphy of retarians, and the beta-tubulin gene duplication occurred before the divergence of Foraminifera and radiolarians. The duplicates have likely been subjected to neofunctionalization responsible for the unique MT to HF assembly/disassembly dynamics, and/or other unknown physiological processes in retarian protists.