Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis

Abstract

Background: Membrane-bound organelles are a defining feature of eukaryotic cells, and play a central role in most of their fundamental processes. The Rab G proteins are the single largest family of proteins that participate in the traffic between organelles, with 66 Rabs encoded in the human genome. Rabs direct the organelle-specific recruitment of vesicle tethering factors, motor proteins, and regulators of membrane traffic. Each organelle or vesicle class is typically associated with one or more Rab, with the Rabs present in a particular cell reflecting that cell's complement of organelles and trafficking routes.

Results: Through iterative use of hidden Markov models and tree building, we classified Rabs across the eukaryotic kingdom to provide the most comprehensive view of Rab evolution obtained to date. A strikingly large repertoire of at least 20 Rabs appears to have been present in the last eukaryotic common ancestor (LECA), consistent with the 'complexity early' view of eukaryotic evolution. We were able to place these Rabs into six supergroups, giving a deep view into eukaryotic prehistory.

Conclusions: Tracing the fate of the LECA Rabs revealed extensive losses with many extant eukaryotes having fewer Rabs, and none having the full complement. We found that other Rabs have expanded and diversified, including a large expansion at the dawn of metazoans, which could be followed to provide an account of the evolutionary history of all human Rabs. Some Rab changes could be correlated with differences in cellular organization, and the relative lack of variation in other families of membrane-traffic proteins suggests that it is the changes in Rabs that primarily underlies the variation in organelles between species and cell types.

Figure 1

Evolutionary tree depicting the relationship of the different Rab families that were potentially present in the last eukaryotic common ancestor (LECA). The tree was constructed as described in the Methods section; we removed any groups that were difficult to place (Rab19, Rab33, Rab34, Rab44 and Rab45) from the tree. Statistical support is shown for edges that support major Rabs groups, or a LECA Rab group, or show unexpected splits, and also for the colored surroundings associated with the edge, with the first number of the pair being the likelihood-mapping value and the second being the almost unbiased test (AU) value [91]. All supergroups are clearly separated, and most LECA groups showed good statistical support. Exceptions generally showed better support in their corresponding supergroup trees (see Additional file 2). For example, the analysis indicated that Rab22 is a close relative of Rab5. Separating Rab5 and Rab22 was complicated by protozoan duplications of Rab5, which have drifted away from their ancestor and are often placed very close to Rab22.

Figure 2

Changes to the repertoire of Rab proteins in the last eukaryotic common ancestor (LECA) considering different hypotheses of rooting the eukaryotic tree. (A-C) This shows the major hypotheses for rooting the eukaryotic tree, and underneath the six different Rab supergroups with their members (order as shown in the key). Presence of a Rab type in the LECA is indicated by a black outline. Hypotheses A and B both suggest the same 20 Rab types being present in the LECA (see also Figure 3 and Additional file 1). Placing Archaeplastida as an outgroup to all other eukaryotes would decrease the number of Rabs in the LECA to a minimum of 14, although in this model the position of Excavata is uncertain [29].

Figure 3

Last eukaryotic common ancestor (LECA) Rabs and their evolution in different phyla. In this overview, we show the changes of LECA Rabs in a number of different phyla. The most elaborate changes to the repertoire are displayed. For example, the transition to metazoan multicellularity gave rise to a large number of new, mainly secretory, Rabs. This can be seen by the change from choanoflagellates (Monosiga brevicollis) to metazoans. Similarly, there was a loss of LECA Rabs in fungi; basal fungi still possess a large number of these Rabs, but Basidiomycota have already lost three and the Saccharomycotina another one. Early in their evolution, plants lost a number of LECA Rabs, but then expanded the remaining Rabs into families. Particularly in plants there was a number of Rabs that we could only locate in one species: Rab24 was found only in the algae Coccomyxa, Rab28 was found only in the algae Micromonas, and for angiosperms we could identify a Rab21 only in Oryza sativa. It seems likely that these groups will get better support once more genome sequences become available.

Figure 4

Overview of how Rab proteins were lost during the expansion of eukaryotes. The losses of the putative last eukaryotic common ancestor (LECA) Rabs are indicated at each evolutionary step, as depicted in the key, with loss being indicated by loss of the black outline. The tree reflects available genome sequences rather than the full diversity of eukaroytic lineages. For the phyla with sufficient sequences available, we depict the losses during the evolution of a specific model organism. The extent of lost LECA Rab types varies considerably between different phyla. Whereas metazoans seem not to have lost any, the Apicomplexa have lost nine. Similarly, humans seem to have only lost two LECA Rabs, but S. cerevisiae has lost a total of fourteen.

Figure 5

Evolutionary history of the human Rabs. Losses and gains of Rabs from the last eukaryotic common ancestor (LECA) towards Homo sapiens. The six supergroups are indicated by their name on the right and the common color scheme. The time points of major remodeling of the human Rab proteins are shown on the top. Most gains in the Rab repertoire are associated with the transition to multicellularity or the rise of vertebrates. In addition, there are two Rab proteins that are specific to primates (Rab40a, Rab40aL), Rab41 is present only in primates and dolphins, and Rab6c seems to be specific to Hominidae. The losses of RabX1, Rab29, RabX4, and RabX6 are indicated by their lines terminating somewhere between the development of multicellularity and the rise of the vertebrates.