Breaking through a phylogenetic impasse: a pair of associated archaea might have played host in the endosymbiotic origin of eukaryotes

Eukaryotic genomes are chimeric in nature, in that they appear to contain genes contributed over time by all three domains of life. A recent analysis of the yeast Saccharomyces cerevisiae genome estimated that approximately 30% of its genes had originated from Bacteria, and about half that number appeared to be eukaryotic innovations, while only around 7% could be linked to archaeal origins [1]. Despite their smaller number, however, the latter category was found to be more essential to viability, more highly expressed, and more connected to protein interaction networks [1]. In general, archaeal-derived genes can be thought of as largely “informational”, while bacterial-derived genes tend to be more “operational”, in that they typically are associated with certain aspects of metabolism [2]. When the human genome is analyzed in a similar fashion, the percent of innovative genes without detectable prokaryotic homologs quadruples to nearly 60%, as might be expected from our increased level of complexity, while the relative proportions of putative bacterial- to archaeal-derived genes becomes even more skewed (36% to 4%, respectively) [3]. Nonetheless, the dichotomy in function as well as overall importance to the cell is still maintained [3]. This leads to a logical question- where did all the prokaryotic-derived genes come from? Evolutionary biologists typically point to horizontal gene transfer and/or endosymbiosis to explain the initial appearance of these genes in eukaryotes. These differ in that the former method is exceedingly common among prokaryotic cells while the latter is so vanishingly rare that it is thought to have occurred only a few times in the 1 to 2 billion years since the last eukaryotic common ancestor (LECA) arose. The notion that mitochondria arose via endosymbiosis of an α-proteobacterial guest has received wide acceptance among biologists [4]. This would suggest that some combination of endosymbiosis and horizontal transfer accounts for eukaryot