Box 1 | The evolutionary link between the Eukarya and the Archaea

From the following article:

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Simonetta Gribaldo, Anthony M. Poole, Vincent Daubin, Patrick Forterre & Céline Brochier-Armanet

Nature Reviews Microbiology 8, 743-752 (October 2010)

doi:10.1038/nrmicro2426

There are numerous features that are specific for eukaryotes and can be traced back to the last eukaryotic common ancestor (LECA), such as the nucleus, the endomembrane system62, 63, 64, the mitochondrion65, 66, spliceosomal introns67, 68, linear chromosomes with telomeres synthesized by telomerases69, meiotic sex70, sterol synthesis71, unique cytokinesis structures72 and the capacity for phagocytosis73, 74. However, the timing, mechanisms and order of events leading to these key cellular and genetic features are unclear. Therefore, knowing the origin of the ancestral lineage leading to the LECA is a key issue.

Since their discovery 30 years ago, the Archaea have been shown to have an evolutionary link with the Eukarya (for an exhaustive early review, see Ref. 75). In particular, many archaeal components of the systems involved in the transmission and expression of genetic information (translation, replication and transcription; also called 'informational systems') show a higher sequence similarity with their eukaryotic homologues than with their bacterial homologues, and in several cases they are absent in the Bacteria. For example, more than 30 ribosomal proteins are specifically shared between the Archaea and the Eukarya but are not present in the Bacteria76, and many archaeal translation factors show similarity to their eukaryotic counterparts77. Archaeal RNA polymerases are closely related to their eukaryotic counterparts, in terms of both subunit composition and structure78, and use very similar promoters and basal transcription factors for initiation79. Finally, the four main activities involved in DNA replication — initiation at the origin, priming of Okazaki fragments, synthesis of the new strands, and DNA unwinding — are carried out by sets of enzymes that are shared between the Archaea and the Eukarya but are not homologous to their bacterial counterparts80, 81. A number of discoveries in the Archaea have confirmed the evolutionary link of their informational systems with those of the Eukarya, such as the presence of small nucleolar RNA-related RNAs that modify ribosomal RNA82, 83, 84, an exosome (for RNA maturation and degradation) with extensive similarity to its eukaryotic counterpart46, 85, and eukaryotic-like histones86, 87.

Several 'operational systems' (that is, systems involved in housekeeping functions) also seem to be related in the Archaea and the Eukarya, including membrane-based systems such as vacuolar ATPases3, secretion pathways46, 88 and a recently identified archaeal cell division system that has homology to the eukaryotic endosomal sorting complex89, 90. Furthermore, the Archaea and the Eukarya may harbour an evolutionary link in their metabolic systems, for example between phosphopantetheine adenylyltransferase in the coenzyme A biosynthesis pathway91 and between carbamoylphosphate synthetase in the pyrimidine and arginine biosynthesis pathway92.

However, the Archaea have many specific characteristics as well. Notably, their membranes are composed of ether-linked lipids, the glycerol phosphate backbone of which has an opposite stereochemistry (glycerol-1-phosphate) with respect to those found in the Bacteria and the Eukarya (glycerol-3-phosphate) and is also synthesized by an unrelated enzyme93. The Archaea also display unique metabolisms such as methanogenesis94, unique enzymes such as specific DNA topoisomerases95 and DNA polymerases96, and unique cell surface structures97, 98.

Finally, the Archaea share several features with the Bacteria, such as the 16S, 23S and 5S ribosomal RNAs, a circular chromosomal architecture (a few exceptions are due to secondary modification99) with an operonic gene arrangement, a coupling between transcription and translation100, and capless translational initiation75.