Chaperonin 60 Phylogeny Provides Further Evidence for Secondary Loss of Mitochondria Among Putative Early-Branching Eukaryotes

Many microbial eukaryotes lack functional mitochondria required for oxidative phosphorylation and instead gain their energy from anaerobic metabolism. Some of these eukaryotes, such as anaerobic ciliates and fungi, have aerobic sister groups with mitochondria and thus are clearly secondary anaerobes (Dore and Stahl 1991; Embley et al. 1995). Other amitochondriate anaerobes, including diplomonads (e.g., Giardia and Spironucleus), microsporidians (e.g., Vairimorpha), parabasalids (e.g., Trichomonas), and pelobionts (e.g., Entamoeba), for which aerobic sister groups have been less readily apparent, were presumed to be representative of the most primitive nucleated cells and to have diverged from other eukaryotes prior to the mitochondrion endosymbiosis (Cavalier-Smith 1983). These lineages were known as Archezoa (Cavalier-Smith 1983) and became the focus of molecular enquiries into the origins and early diversification of eukaryotes. However, one result of these studies was that the Archezoa hypothesis was rejected on a case-by-case basis, as it was demonstrated that archezoans arose from within groups which possessed mitochondria or that they contained genes derived from the mitochondrial endosymbiont (reviewed in Embley and Hirt 1998; Roger 1999). The strongest datum rejecting the Archezoa hypothesis for diplomonads is the report of a mitochondrial chaperonin 60 (cpn60) gene (cpn60) on the genome of Giardia lamblia (Roger et al. 1998). In aerobic eukaryotes, cpn60 plays an important role in mitochondrial protein import (Martin 1997), and its phylogeny reflects an a-proteobacterial ancestry consistent with an origin from the mitochondrion endosymbiont (Viale and Arakaki 1994). The cpn60 gene is found on the host nuclear genome, which is usually interpreted as indicating that it was transferred from the mitochondrial symbiont to the host nucleus early in the history of that symbiosis (Viale and Arakaki 1994). Thus, a reasonable explanation for the presence of cpn60 genes on the genome of Giardia would be that it too is descended from ancestors that once contained the mitochondrion endosymbiont. In contrast, several recent publications have suggested that Giardia may still be a true archezoan but one which has acquired mitochondrial-like genes through horizontal gene transfer (HGT) events independent of the mitochondrial endosymbiosis (Sogin 1997;