Use of higher order characters example of ATPases

The use of ATPase catalytic and non-catalytic subunits to root the tree of life was originally introduced by Gogarten et al. (1989). This pair of anciently duplicated genes places the root on the branch leading to Bacteria with high confidence (see Figure 9.3). Either the catalytic or the non-catalytic subunits can be considered

186 Horizontal gene transfer, gene histories, and the root of the tree of life Present

Steady State: Rate of speciation approx. balanced by rate of extinction

Diversification/ Expansion

Origin of Life

Prebiotic Evolution

186 Horizontal gene transfer, gene histories, and the root of the tree of life Present

Steady State: Rate of speciation approx. balanced by rate of extinction

Diversification/ Expansion

Origin of Life

Prebiotic Evolution

Most Recent Common Ancestor

Fig. 9.2. Schematic depiction of a model for the tree/corral of life highlighting the position of the most recent common ancestor. Extinct lineages are shown in grey. Extant lineages at the tip of the tree are traced back to their last common ancestors (in black).

Most Recent Common Ancestor

Fig. 9.2. Schematic depiction of a model for the tree/corral of life highlighting the position of the most recent common ancestor. Extinct lineages are shown in grey. Extant lineages at the tip of the tree are traced back to their last common ancestors (in black).

as the ingroup, and the outgroup is provided by the paralogous subunits. The outgroup, a set of sequences rather divergent from the ingroup, joins the ingroup on the longest internal branch. While this placement of the root is recovered using different methods and evolutionary models (Gogarten et al., 1989; Iwabe et al., 1989), it also coincides with the place where the root would be located as the result of the LBA artefact (Philippe and Forterre, 1999; Gribaldo and Philippe, 2002). However, in the case of the ATPases higher order characters exclude placing the outgroup within the archaeal/eukaryotic ATPases subunits (no higher order characters have been recognized for bacterial F-ATPases). The archaeal vacuolar ATPase non-catalytic subunits have lost the canonical Walker motif GxxGxGKT in their ATP binding pocket (Gogarten et al., 1989). This motif is present in the orthologous F-ATPase non-catalytic subunits as well as in all of the ancient paralogues, including the paralogous Rho transcription termination factors (Richardson, 2002) and ATPases involved in assembly of the bacterial flagella

Non-Catalytic Subunits

Bacterial F-ATPase Alpha subunit

Archaea/ Eukaryotes ATPase subunit B

Bacterial F-ATPase Beta subunit

Catalytic Subunits

Archaea/ Eukaryotes ATPase subunit A

Fig. 9.3. Schematic tree showing the evolution of catalytic and non-catalytic subunits of ATPases (for detailed phylogeny see Fig. 2 in Zhaxybayeva et al. (2005)). Higher order characters are mapped to the branch leading to the clade where all the members of the clade possess the character. See text for more details.

(Vogler et al., 1991). Similarly, the catalytic subunits of the archaeal and of the eukaryotic vacuolar type ATPase contain a faster evolving 'non-homologous' region that has no counterpart in the catalytic F-ATPase subunits, nor is this region found in any of the non-catalytic subunits (Zimniak et al., 1988; Gogarten et al., 1989). The absence of the canonical Walker motif in the regulatory subunits and the presence of the non-homologous region in the catalytic subunits thus are shared derived characters of the vacuolar and archaeal ATPases that preclude moving the root of the ATPase phylogeny to a place within the clade constituted by the archaeal and eukaryotic ATPases.

Was this article helpful?

0 0

Post a comment