A new fusion hypothesis for the origin of Eukarya, better than previous ones, but probably also wrong
This paper from Patrick Forterre summarizes his current thoughts. However, one needs to first read Bill Martin’s review paper before venturing into specific hypotheses.
I discuss here the possibility that Eukarya originated from the engulfment of a thaumarchaeon by a PCV (Planctomycetes, Verrucomicrobia, Chlamydiae) bacterium, followed by invasions of NCLDV and retroviruses. The thaumarchaeon provided both informational and operational proteins (actins, ESCRT proteins), including some essential proteins absent in other archaeal phyla (Topo IB), whereas the PVC bacterium provided phospholipids, tubulin and the membrane coat proteins required for the formation of the nucleus. Viral invasions introduced many proteins that are specific to modern Eukarya and produced an arms race that favoured the evolution of Eukarya toward increasing complexity. This scenario is the best possible fusion hypothesis that can be presently proposed. However, it still requires several ad hoc assumptions to explain the origin of the nucleus and the distribution pattern of archaeal and bacterial traits in modern Eukarya. Furthermore, it still fails to explain convincingly the origin of eukaryal viruses and the existence of three distinct lineages of ribosomes. I conclude that Eukarya and their viruses more probably evolved from a specific lineage, according to the three domains scenario originally proposed by Carl Woese.
Bill Martin’s criticism (119 refers to above paper) -
In the age of genomes, even supporters of the phagotrophic theory had to account for the circumstance that eukaryotes had archaebacterial informational genes, but preferably without extensive and specific rate fluctuations protein sequence evolution of the quantum evolution type hard-wired into the theory. Hence a second and popular solution to the origin of informational and operational genes was to suppose that eukaryote evolution, presumably one that gave rise to the nucleus, usually presumed to have arisen in a eubacterial host. Several variants on this theme emerged [112-118], and continue to emerge [119]. Those theories have at least three major problems in common. First, and in contrast to chloroplasts and mitochondria, the nuclear compartment is in no way homologous to a prokaryotic cell, hence the whole (100 year old) notion that the nucleus was ever an endosymbiont is tenuous to begin with [120]. As with the flagellum [121] or microbodies [122], there is no evidence or homology at all to suggest that the nucleus is descended from an symbiotic bacterium. Second, they derive a cell that has eubacterial genome and eubacterial ribosomes in the cytosol, with the informational genes locked up within the archaebacterial endosymbiont. No formulations of nucleosymbiotic origins to date, even the most recent [119], provides any sound rationale as to how we arrive at a state where the ancestral eubacterial ribosomes and genome in the cytosol are gone and the archaebacterial ribosomes are operating in the cytosol while the archaebacterial chromosomes
are retained in the nucleus. Third, theories for an endosymbiotic origin of the nucleus suffer, like the phagotrophic theory, from the circumstance that they all
educe, as their crucial intermediate, a eukaryote that primitively lacks mitochondria (an archezoon), thereby predicting that primitively mitochondrion-lacking groups should still be around today. Contrary to that prediction, it has turned out that all eukaryotic groups either once possessed or still possess mitochondria, either in the form of O2-respiring mitochondria, anaerobic mitochondria, hydrogen-producing mitochondria (hydrogenosomes) or highly reduced mitochondria (mitosomes) [123-129]. Nucleosymbiotic origin theories keep cropping up in new garb, probably because none of them really account for the observations and remain unconvincing, sometimes even to their proponents [119].
