Early one celled common ancestor of eubacteria, archaebacteria and eukaryotes is
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It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.
1. Introduction
Archaea have been confused with bacteria, under the term prokaryotes, until their originality was finally recognized by 16S rRNA cataloguing [1]. Archaea were previously “hidden before our eyes”, strikingly resembling bacteria under the light and electron microscopes. Archaea and bacteria are also quite similar at the genomic level, with small circular genomes, compact gene organization, and functionally related genes organized into operons. At the same time, archaea, unlike bacteria, exhibit a lot of “eukaryotic features” at the molecular level [2–6]. It is often assumed that archaea resemble eukarya when their informational systems (DNA replication, transcription, and translation) are considered but resemble bacteria in terms of their operational systems. This is clearly not the case, since many archaeal operational systems (such as ATP production, protein secretion, cell division and vesicles formation, and protein modification machinery) also use proteins that have only eukaryotic homologues or that are more similar to their eukaryotic rather than to their bacterial homologues [7–14]. The bacterial-like features of some archaeal metabolic pathways could be mostly due to lateral gene transfer (LGT) of bacterial genes into Archaea, driven by their cohabitation in various biotopes [15]. Indeed, beside bacterial-like genes possibly recruited by LGT, metabolic pathways in archaea—such as the coenzyme A or the isoprenoid biosynthetic pathways—also involve a mixture of archaea-specific and eukaryotic-like enzymes [16–18]. Archaea and eukarya share so many features in all aspects of their cellular physiology and molecular fabric that eukaryotes cannot be simply envisioned as a mosaic of archaeal and bacterial features. Archaea and eukarya clearly share a more complex evolutionary relationship that remains to be understood.
Whereas many eukaryotic a also fundamentally differ from eukarya in the nature of their membranes (with a unique type of lipids in archaea), and the type of viruses infecting them. The problems raised by the evolution of membranes have been nicely reviewed recently by Lombard et al. and I will refer to their work later on to discuss different models for the origin of archaea [22]. In contrast, the problem raised by the drastic differences between archaeal and eukaryotic viruses has never been really discussed. For instance, Martijn and Ettema never mentioned the word virus in their review on the origin of eukaryotes [21]. Viruses are also completely absent from the papers of Cavalier-Smith or Carl Woese himself. This is probably because, as recently stated by Koonin and Wolf, “viruses are no part of the traditional narrative of evolutionary biology”