% Before the discovery of the Lokiarchaeota, symbiogenetic models proposing a direct endosymbiosis of the mitochondrial ancestor within one archaeon had gained popularity [24,26,50] (Figure 2B). They imply a triggering effect of eukaryogenesis for mitochondrial endosymbiosis. However, the fact that the newly discovered archaea possess several homologs to membrane remodeling and cytoskeleton-related eukaryotic proteins has opened the possibility for a proto-eukaryotic lineage endowed with phagocytosis to evolve from within archaea, which seems to be the currently favored hypothesis [9,10]. In this case, mitochondria would incorporate later (Figure 2A). The difference between the two situations is far from irrelevant because the driving forces underlying eukaryogenesis and the predictions of the two models are very different. In the former case, mitochondrial symbiosis would be the cause of eukaryogenesis; in the latter, the consequence. In the former case, amitochondriate eukaryotes would have never existed; in the latter, the possibility that archaea-derived amitochondriate proto-eukaryotes exist is real. In models invoking a bacterial host for the archaeon (Figure 2C), the mitochondrial symbiosis is a second, independent event; mitochondria would therefore come later, but, as in the case of autogenous models, the time between the start of eukaryogenesis and the mitochondrial stabilization is difficult to determine. The strong alphaproteobacterial signal in eukaryotic genomes [33,51] would tend to suggest a relatively late mitochondrial incorporation event.
% The origin of the nucleus remains mysterious. While it was present in LECA, and evolved as part of the endomembrane system involving many protein components of archaeal and bacterial ancestry [52], most models do not provide any (or any convincing) selective force for the evolution of this defining character. Two driving forces have been evoked by autogenous models. Cavalier-Smith proposed that the nucleus evolved to prevent DNA damage caused by cytoskeletal pulling [53], an idea adopted by others [26]. However, eukaryotic chromosomes are able to overcome mechanical stresses during mitosis, when the nuclear envelope disintegrates in many protists, and even in species where the chromosomes are permanently uncondensed. In addition, eukaryotes (as do prokaryotes) have efficient DNA repair systems to cope with single- and double-strand breaks occurring during the mechanically-challenging DNA-dependent processes (replication, transcription, recombination), and many eukaryotes have genomes with several dozens of chromosomes, which reduces the individual size of DNA molecules, diminishing breakage probability. JÃ©kely proposed that the nucleus appeared to safeguard ribosome biogenesis, preventing the formation of chimeric ribosomes during mitochondrial endosymbiosis [54]. However, the formation of chimeric ribosomes could have been more simply achieved by retaining the ribosomal protein genes in the mitochondrial genome, as is the case with the ribosomal RNA and other protein genes for which cytosolic synthesis and transport back to the mitochondrion poses a problem.
% In the framework of the hydrogen hypothesis, the nucleus was proposed to appear de novo through the synthesis of bacterial-like lipids that would form vesicles in the archaeal cytoplasm (Figure 2B). The nuclear compartment would have evolved to decouple transcription and translation, thus preventing the synthesis of aberrant proteins as introns appeared [55]. However, this explanation is at odds with the fact that a single intron in an essential gene is deleterious if transcription and translation are not already uncoupled and a splicing system is not in place. Thus, the decoupling of transcription and translation by the nuclear membrane must precede intron invasion. Such an idea was put forward in the framework of the syntrophy hypothesis, which proposes the endosymbiotic origin of the nucleus [31] (Figure 2C). Endosymbiotic models for the origin of the nucleus easily account for the presence of a different compartment [21,28,31], but the difficulty here lies in how to explain what drives the endosymbiosis and the origin of the endomembrane system
% http://www.sciencedirect.com/science/article/pii/S0169534715002384?via%3Dihub#bib0535
% It possessed all the paradigmatic eukaryotic features, including the nucleus (with nuclear lamina and nuclear pores), a complex endomembrane system, and a sophisticated tubulin/actin-based cytoskeleton. In relation to the endomembrane system, LECA possessed developed endocytic and exocytic pathways as well as concomitant vesicle-trafficking networks (including Golgi apparatus, lysosomes, and autophagosomes) which also involved the cytoskeleton. The cytoskeleton was also essential for phagocytosis, and the presence of this mechanism indicates that LECA was most likely heterotrophic and fed on organic matter, perhaps as a predator of other cells. Its metabolism was most likely aerobic because it possessed oxygen-respiring mitochondria. The cytoskeleton had also a key role in mitosis, cell cytokinesis, and cell motility (probably by several flagella). Meiosis was likely present, opening the possibility for some form of sexual reproduction. The genome contained introns, making necessary a splicing system, likely integrated in a sophisticated gene regulation machinery that also included the activity of small non-coding RNAs and RNA interference. This list is not exhaustive because many other processes, such as ubiquitination and proteasome-mediated degradation, were also present. Coding for all those characters, some of them based on the participation of hundreds of different proteins, requires a very large number of genes. Conservative estimates suggest that the eukaryotic ancestor had a genome with at least 4000â€“5000 genes [52,79]. This implies that LECA was complex, fully comparable to many modern eukaryotes, and that the toolkit for eukaryotic cell components was established very early.
% Alphaproteobacterial genomes range from âˆ¼1.3 Mb (parasitic Rickettsia and free-living Pelagibacter spp.) to >9 Mb, but the largest mitochondrial genomes have only âˆ¼100 genes (some excavate protists) and the smallest â€“ animal and apicomplexan mitochondrial genomes â€“ have only 13 and 3 protein-coding genes, respectively. Genome extinction was achieved in many hydrogenosomes and other mitochondria-related organelles (MROs) found in some parasitic and/or anaerobic protists [4,77,82]. 

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