Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton

Abstract

Background: The genesis of the eukaryotes was a pivotal event in evolution and was accompanied by the acquisition of numerous new cellular features including compartmentalization by cytoplasmic organelles, mitosis and meiosis, and ciliary motility. Essential for the development of these features was the tubulin cytoskeleton and associated motors. It is therefore possible to map ancient cell evolution by reconstructing the evolutionary history of motor proteins. Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA).

Results: We bioinformatically identified 1624 putative kinesin proteins, determined their protein domain architectures and calculated a comprehensive Bayesian phylogeny for the kinesin superfamily with statistical support. These data enabled us to define 51 anciently-derived kinesin paralogs (including three new kinesin families) and 105 domain architectures. We then mapped these characters across eukaryotes, accounting for secondary loss within established eukaryotic groupings, and alternative tree topologies.

Conclusions: We show that a minimum of 11 kinesin families and 3 protein domain architectures were present in the LCEA. This demonstrates that the microtubule-based cytoskeleton of the LCEA was surprisingly highly developed in terms of kinesin motor types, but that domain architectures have been extensively modified during the diversification of the eukaryotes. Our analysis provides molecular evidence for the existence of several key cellular functions in the LCEA, and shows that a large proportion of motor family diversity and cellular complexity had already arisen in this ancient cell.

Figure 1

Distribution of ancient kinesin paralogs in 45 diverse eukaryotes. Using the results of our comprehensive kinesin motor domain phylogeny (Additional file 2) we identified 51 kinesin paralogs, encompassing 17 kinesin families and 34 subfamilies. Presence of paralog(s) in a genome is indicated by a filled circle, absence/not-found is indicated by an open circle. Only paralogs from well-supported nodes were considered (p > 0.95 by both aLRT methods; see Additional file 2). Dark blue circles indicate presence of members of a full kinesin family (corresponding to the deepest well-supported nodes for kinesin groups containing sequences from eukaryotes belonging to more than one eukaryotic "supergroup"), whilst subfamily paralogs are indicated by light blue circles beneath (suffixed A, B, C etc.). Kinesins falling within a particular kinesin family, but outside of all the contained well-supported subfamilies are suffixed '-X' (e.g. Kinesin-1-X). Groups of kinesins that do not have sufficient membership to be considered full kinesin families (see Results and Discussion) are numbered X1 to X14 (green circles). Species analyzed are grouped into higher taxonomic groups. Paralog families used in Dollo parsimony analyses are marked 'c' (character) adjacent to the first column.

Figure 2

Distribution of kinesin protein architectures in 45 diverse eukaryotes. Pfam and CDD searches were used to identify putative gene architectures for the 1624 kinesin proteins identified in the genome datasets. All unique gene architectures identified in two or more genomes are shown here while all 105 different gene architectures identified are shown in Additional file 4. Presence of a gene architecture in a genome is indicated by a filled circle, absence/not-found is indicated by an open circle. Species analyzed are grouped into higher taxonomic units. Architectures used in Dollo parsimony analyses are marked 'c' (character), while architectures, which appeared not to be homologous based on further investigation (see Additional file 6), are marked 'd(ex)' (discounted and excluded), while this analysis adjusted the taxon distribution of some architecture characters marked 'd/c' (discounted and corrected) adjacent to the first column. Domains found more than once are numbered to indicate the multiples in which the domains are found (e.g. x2-7 indicates the protein contained between 2 and 7 copies of the domain).

Figure 3

Defining the kinesin repertoire of the last common eukaryotic ancestor (LCEA). We considered 5 rooted eukaryotic trees to infer conservative estimates of the minimal ancestral repertoire of kinesins present in the LCEA using Dollo parsimony: A) 'Metamonada-first'; B) 'Discicristata-first'; C) 'Excavata-first'; D) root between unikonts and bikonts; E) Dollo most parsimonious tree necessary to explain the extant distribution (boxed in red). The unconstrained most parsimonious tree gives an unrealistic eukaryotic tree topology and therefore is likely to underestimate the LCEA repertoire (see Results and Discussion). The parsimony scores under the two alternative datasets are shown for all 5 topologies. Also shown are the results of SH alternative topology tests for the four alternative models under the polytomy favored by the analysis of Burki et al. [26] (see Results and Discussion). Paralog families and kinesin architectures, which must have been present in the LCEA given the tree topology are shown beneath each tree. Kinesin paralogs are colored blue for families (K1-20) and green for non-families (X1-14; see Figure 1). Kinesin protein domain architectures are shown in black (see Figure 2). These analyses indicate minimally 18 to 29 kinesin characters (paralogs/architectures) in the LCEA. Kinesin characters present in the LCEA under the 4 leading models of the eukaryotic tree topology, A-D (the minimal ancestral repertoire - MAR) are marked in bold.