Wadsworth Center, New York State Department of Health.
Mol Biol Evol. 2013 Nov;30(11):2487-93. doi: 10.1093/molbev/mst150. Epub 2013 Sep 4.
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" β-tubulin (β2) is critically involved in forming helical filaments (HFs), a unique microtubule (MT) assembly/disassembly intermediate found in foraminiferan reticulopodia. Such noncanonical β-tubulin sequences have also been found in two radiolarian species and appear to be closely related to the foraminiferan β2. In this study, we report 119 new β-tubulin transcript sequences from six foraminiferans, four radiolarians, and a related non-retarian species. We found that foraminiferan and radiolarian β2-tubulins share some of the unusual substitutions in the structurally essential and usually conserved domains. In the β-tubulin phylogeny, retarian β2-tubulin forms a monophyletic clade, well separated from the canonical β-tubulin (β1) ubiquitous in eukaryotes. Furthermore, we found that foraminiferan and radiolarian β2-tubulin lineages were under positive selection, and used homology models for foraminiferan α- and β-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 α- and β-tubulin heterodimers. Our results indicate that the unusual β2-tubulin is a molecular synapomorphy of retarians, and the β-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.
有孔虫和放射虫是密切相关的变形虫（即肉足虫），通常以其壳和伪足为特征。先前的研究假设不寻常的“类型 2”β-微管蛋白（β2）在形成螺旋丝（HFs）中起着至关重要的作用，这是一种在有孔虫类网状伪足中发现的独特微管（MT）组装/拆卸中间产物。这种非典型的β-微管蛋白序列也在两种放射虫物种中发现，似乎与有孔虫β2密切相关。在这项研究中，我们从六个有孔虫、四个放射虫和一个相关的非肉足虫物种中报告了 119 个新的β-微管蛋白转录序列。我们发现有孔虫和放射虫的β2-微管蛋白在结构上必需且通常保守的区域中共享一些不寻常的取代。在β-微管蛋白系统发育中，肉足虫β2-微管蛋白形成一个单系群，与真核生物中普遍存在的典型β-微管蛋白（β1）明显分开。此外，我们发现有孔虫和放射虫的β2-微管蛋白谱系受到正选择的影响，并使用有孔虫α-和β-微管蛋白六聚体的同源模型来理解正选择取代的结构影响。我们认为，正选择取代通过改变α-和β-微管蛋白异二聚体之间的侧向和纵向相互作用，在 MT 向 HF 的转变中起着关键作用。我们的结果表明，不寻常的β2-微管蛋白是肉足虫的分子同源特征，β-微管蛋白基因的复制发生在有孔虫和放射虫分化之前。这些副本可能经历了新功能化，负责独特的 MT 向 HF 的组装/拆卸动力学，和/或肉足虫原生动物中其他未知的生理过程。
