Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution

Abstract

The process by which some eukaryotic organelles, for example the endomembrane system, evolved without endosymbiotic input remains poorly understood. This problem largely arises because many major cellular systems predate the last common eukaryotic ancestor (LCEA) and thus do not provide examples of organellogenesis in progress. A model is emerging whereby gene duplication and divergence of multiple "specificity-" or "identity-" encoding proteins for the various endomembranous organelles produced the diversity of nonendosymbiotically derived cellular compartments present in modern eukaryotes. To address this possibility, we analyzed three molecular components of the endocytic membrane-trafficking machinery. Phylogenetic analyses of the endocytic syntaxins, Rab 5, and the beta-adaptins each reveal a pattern of ancestral, undifferentiated endocytic homologues in the LCEA. Subsequently, these undifferentiated progenitors independently duplicated in widely divergent lineages, convergently producing components with similar endocytic roles, e.g., beta1 and beta2-adaptin. In contrast, beta3, beta4, and all other adaptin complex subunits, as well as paralogues of the syntaxins and Rabs specific for the other membrane-trafficking organelles, all evolved before the LCEA. Thus, the process giving rise to the differentiated organelles of the endocytic system appears to have been interrupted by the major speciation event that produced the extant eukaryotic lineages. These results suggest that although many endocytic components evolved before the LCEA, other major features evolved independently and convergently after diversification into the primary eukaryotic supergroups. This finding provides an example of a basic cellular system that was simpler in the LCEA than in many extant eukaryotes and yields insight into nonendosymbiotic organelle evolution.

Fig. 1.

Phylogenetic analysis of SynE genes with long-branch taxa removed, showing lineage-specific duplications in vertebrates and flowering plants. The inner box illustrates the timing of the duplication in those clades, whereas the outer box shows the well resolved preduplicates supporting that duplication. Nodes supporting clades of note are bolded. In this and subsequent phylogeny figures, node support values are given in the order of Bayesian posterior probabilities, PhyML bootstrap percentages, ML distance-corrected bootstrap percentages, and RaxML bootstrap percentages. Values are given for all nodes supported by >0.80 PP and >50% bootstrap support in two of three other methods. A star denotes a node supported by >0.95 posterior probability and >95% bootstrap support in two of three other methods. The − illustrates that the clade of interest was not reconstructed by the relevant method.

Fig. 2.

Phylogeny of SynE homologues that have been functionally characterized as associated with the early or late endocytic pathways. This clearly resolves the homologues into lineage-specific and not organellar clades. EE, associated with early endosomes or PVC; LE, associated with lysosome/vacuole.

Fig. 3.

Phylogenetic analysis of Rab 5 sequences. Shown is the phylogenetic analysis of Rab 5 homologues with long-branch taxa removed. The independent duplication of Rab 5 homologues in vertebrates (node value in bold) with the duplicate clades marked by the inner box and the node supporting their monophyly marked by the outer box is shown. Similar duplications are likely to have occurred in the kinetoplastids (SI Fig 10); the placement of the O. tauri Rab 5B homologue is likely a result of long-branch attraction. Similar gene duplications may well have occurred in the fungi and Viridiplantae. However, in the latter two lineages, although the pattern is suggestive, it is not possible to state with certainty because of the lack of phylogenetic resolution.

Fig. 4.

Phylogenetic analysis of the β1/2 clade. The lineage-specific duplicates are robustly resolved in Arabidopsis, in the vertebrates, and in the kinetoplastids (nodes shown in bold). The asterisks in the support values for the Viridiplantae denotes the fact that although the full clade of streptophytes and green algae is not reconstructed by PhyML and ML distance methods, a clade of the single O. sativa as an outgroup to the two A. thaliana duplicates is supported by 92% and 100%, respectively. This supports the conclusion of an independent duplication giving rise to β1- and β2-subunits in this lineage. Here, the inner box denotes the duplicate clades; the outer box illustrates the node supporting monophyly of the duplicates.

Fig. 5.

Evolution of endocytic organelles with rabs and syntaxins. The phylogenetic data here are most consistent with the endocytic system having evolved by the process of autogenous organelle evolution illustrated in SI Fig. 6 but being interrupted by the eukaryotic big bang. A single undifferentiated endocytic compartment would have initially been serviced by both undifferentiated endocytic rabs and syntaxins. The rabs duplicated and diverged before the eukaryotic big bang, however the endocytic syntaxins did not. Post-LCEA SynE and Rab 5 continued the trajectory of gene duplication and functional divergence, yielding increased specificity of function.