Question 6. Based On Your Drawing, How Many Genomes Were Present In Leca?
Trends Ecol Evol. Author manuscript; available in PMC 2022 Nov x.
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PMCID: PMC4640172
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Open questions on the origin of eukaryotes
Abstruse
Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was circuitous and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the contempo discovery of an archaeal lineage phylogenetically shut to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more than comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of primal eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.
Keywords: eukaryogenesis, archaea, symbiosis, origin of nucleus, metabolism, syntrophy, membrane
A long-lasting query
The origin of the eukaryotic cell was a major evolutionary event that led to a wide diversification of lineages displaying very different morphologies, several of which independently evolved towards multicellularity [1]. Compared to the average prokaryotic cell, the average early eukaryotic jail cell represented a considerable increase in structural complication, typified by the presence of an endomembrane organization delimiting a hallmark eukaryotic feature, the nucleus, and membrane-bound organelles, notably mitochondria. In the past decades progress in prison cell and molecular biological science, microbial multifariousness studies and, most of all, comparative genomics and molecular phylogeny, have helped to ameliorate constrain the nature of that transition. Several facts related to the early evolution of eukaryotes take been unambiguously established including, amidst others, a mixed archaeal-bacterial legacy in eukaryotic genomes (see Glossary; Box 1). It is at present clear that the last eukaryotic common ancestor (LECA) was a rather complex organism already possessing major idiosyncratic features associated with extant eukaryotes (Box 2). It is as well recognized that endosymbiosis did play a crucial office in eukaryogenesis and that the evolution of the alphaproteobacterial endosymbiont at the origin of mitochondria contributed the basics of energy metabolism [2,3] and largely shaped the eukaryotic genome [4], leading to innovations (Box iii). While more detailed knowledge almost the last common eukaryotic ancestor and the alphaproteobacterial ancestor of mitochondria is yet needed, the almost key open up query relates to the nature of the host that acquired the mitochondrial antecedent and the eukaryogenic process itself. This is the indicate upon which most models for the origin of eukaryotes take traditionally diverged [5-viii]. The recent discovery of an archaeal lineage, the Lokiarchaeota, sharing more, and seemingly more than closely related, genes with eukaryotes [9] represents a significant advance towards the understanding of eukaryotic origins. From the phylogenomics perspective, this observation supports an archaeon as (or an archaeal contribution to) the host of mitochondria [10]. However, from the mechanistic perspective, this solution renovates fundamental open questions that chronicle to the specific evolutionary procedure and the underlying selective drivers at the origin of key eukaryotic features. In the following, nosotros very briefly recapitulate the general types of current eukaryogenic models, exposing central mechanistic questions that demand to be answered in order to constrain and/or test those hypotheses.
Mechanistic types of eukaryogenesis models
Many dissimilar hypotheses for the origin of eukaryotes accept been proposed (for some reviews, see [v-8]). Here, we briefly highlight mechanisms proposed past the 2 principal general types of eukaryogenesis models. Many models exclusively focus on the phylogenetic ancestry of eukaryotes, looking for their closest prokaryotic relatives, or on particular mechanistic details, just but a few models provide combined phylogenetic and mechanistic frameworks.
Autogenous models
For autogenous (or endogenous) hypotheses, eukaryotes descend from a proto-eukaryotic lineage in which near typical eukaryotic properties had already evolved prior to the acquisition of mitochondria, notably a circuitous endomembrane system, including the nucleus, and a developed cytoskeleton. Those two components were essential for the evolution of phagocytosis, a critical property that subsequently allowed the engulfment of the mitochondrial ancestor. Although for some authors that proto-eukaryotic lineage was bequeathed and retained primitive characters [xi,12] (Figure one.A), for the bulk, information technology was sister to the archaea (Figure 1.B). This would explain the archaeal-similar features of 'informational' processes in eukaryotes [five,13]; the bacterial-similar 'operational' genes would derive from mitochondria. This was, until recently, the well-nigh popular model. A radical variant is the Neomura hypothesis, proposing that the protoeukaryotic lineage sister to archaea formed a clade with Gram positive bacteria (Actinobacteria and Firmicutes) nested inside the remaining, Gram negative bacteria [14]. The emergence of a proto-eukaryotic lineage from inside bacteria and, more than specifically, Planctomycetes, has too been proposed based on the presence of endomembranes in members of this lineage [xv]. Notwithstanding, this hypothesis fails to explain the archaeal-similar features constitute in eukaryotes. In addition, many different leaner have endomembranes, generally to compartmentalize metabolic regions in the cytoplasm [16]. A very well-known instance is that of cyanobacterial thylakoids. Indeed, prior to the general acceptance of the endosymbiotic theory for chloroplasts and mitochondria, cyanobacteria were evoked as eukaryotic ancestors precisely because of their power to generate endomembranes [17]. Every bit for Planctomycetes[eighteen], these are cases of analogy showing that producing endomembranes is feasible and common amidst prokaryotes.
Schematic summary of general types of hypotheses on the phylogenetic origin of eukaryotes in the tree of life before and after the discovery of Lokiarchaeota and related deep-branching archaea. A, archaea; B, bacteria; Due east, eukaryotes. The schematic organelle drawing represents the mitochondrial acquisition.
Symbiogenetic models
A large category of hypotheses of increasing popularity contends that eukaryotes derive straight from symbiosis betwixt archaea and bacteria, refusing the existence of a third, independent proto-eukaryotic lineage for which direct testify is missing. Thus, there would be simply two chief phylogenetic domains (leaner and archaea), eukaryotes existence mergers (a secondary domain). Originally judged mechanistically unlikely based on the lack of phagocytosis in prokaryotes (hence, the impossibility to acquire endosymbionts), the discovery of endosymbionts within leaner [19], together with the discovery of membrane remodeling in leaner and archaea [16,20], made this endosymbiotic procedure plausible. Margulis recovered the thought of an endosymbiotic origin of organelles from Mereschkowski's pioneer proposal [21] and further hypothesized that eukaryotic flagella derive from symbiotic spirochetes (series endosymbiotic theory) [22]. The rest of symbiogenetic models tin be more often than not classed in ii categories. Ane states that the endosymbiosis of the alphaproteobacterial ancestor of mitochondria inside one archaeon triggered eukaryogenesis (Effigy 1.C). Searcy suggested a metabolic symbiosis mediated by sulfur transfer in a wall-less Thermoplasma-like (belonging to the Euryarchaeota, one of the ii major archaeal branches) archaeon [23]. The hydrogen hypothesis is the most elaborate of these models; here, the symbiosis was driven by interspecies hydrogen transfer to a methanogenic archaeon (Euryarchaeota) [24]. Afterwards, dissimilar archaeal hosts for the mitochondrial ancestor accept been proposed based on gene content and molecular phylogenetic analyses of after discovered archaea, including members of the recently recognized TACK superphylum (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) [25,26] or deep-branching archaea [27]. The second group of symbiogenetic models posits the endosymbiotic origin of the nucleus, which would derive from the endosymbiosis of one archaeon inside a bacterium. The acquisition of mitochondria would constitute a second, independent symbiotic issue (Effigy 1.D). Some models posit that the nucleus derived from an endosymbiotic eocyte archaeon within a Gram negative bacterium [28] or from 1 archaeon within a gammaproteobacterium [29] based on gene content and phylogenetic analyses, merely fail to provide whatsoever articulate selective advantage for the nuclear endosymbiosis. The syntrophy hypothesis proposes a highly detailed mechanism suggesting that eukaryotes evolved from a two-stride symbiosis. A methanogen would have first established a hydrogen-mediated metabolic symbiosis with a fermentative ancestral myxobacterium (Deltaproteobacteria); mitochondria would derive from metabolically versatile, facultative aerobic alphaproteobacteria [30,31].
Lokiarchaeota come into play
Until recently, attempts to test the different hypotheses and pinpoint the nature of the mitochondrial host based on phylogenomic assay with increasingly improved methods and taxonomic sampling led to contradictory and/or inconclusive results [32,33]. More recent analyses raised serious suspicions that eukaryotes might branch within i of the 2 major archaeal branches [34] and be a secondary domain[35] resulting from the merging of archaeal and bacterial lineages. At the same time, many ecology lineages in the 2 major archaeal clades, the Euryarchaeota and the TACK superphylum or Proteoarchaeota [36], were known past their 16S rRNA sequences, merely their genomes remained largely inaccessible until the advent of metagenomics and single cell genomics. Recently, genomic information assembled from seemingly eukaryote-free deep-sea sediment metagenomes for one environmental lineage branching deeply inside the TACK superphylum, the Lokiarchaeota, reveals a somewhat larger repertoire of genes in common with eukaryotes than the residual of known archaea, in particular genes involved in membrane remodeling and the cytoskeleton [9]. Eukaryotes branch as sister of this archaeal group in phylogenomic analyses, suggesting the eukaryogenic interest of an ancestral archaeon belonging to this lineage or of a yet-to-discover archaeal lineage with an even richer eukaryotic-like gene content.
Relatively little is still known from this environmental lineage. Previous microbial environmental and geochemical analyses show that members of this clade (also known as Deep Sea Archaeal Group –DSAG– or marine benthic group B) are diverse and occur in various anoxic settings, often dominating in marine deep-subsurface sediments [37-39]. They appear to exist very small (<1 μm diameter) as shown by fluorescence in-situ hybridization and their presence in sediment cores correlates with that of typical ether-linked isoprenoid lipids, strongly suggesting typical archaeal membranes [37,38]. Stable isotope analyses suggest that they are involved in the anaerobic degradation of sedimentary organic matter, a procedure in which intricate syntrophic interactions involving fermentation of circuitous organics and subsequent reactions leading to CHiv or CO2, depending on the syntrophic partners. It has been suggested that these archaea might participate in dissimilatory CH4 oxidation [37] or iron or manganese reduction[38].
While the discovery of Lokiarchaeota rules out the existence of a third proto-eukaryotic lineage independent of leaner and archaea (Effigy i.A-B), further supporting the existence of only 2 principal domains [10], it is still compatible with three dissimilar models for the origin of eukaryotes (Figure one.E-K) that imply three distinct mechanisms (Figure ii). One corresponds to the classical autogenous model invoking a proto-eukaryotic lineage transposed to 1 specific subgroup of the archaea, and is the view that seems favored by several authors [9,x]. Here, an extensive endomembrane system and cytoskeleton would have evolved in an archaeon, leading to the emergence of a proto-eukaryotic lineage of archaeal origin (Figure ii.A). The two other models would imply endosymbiosis of the mitochondrial ancestor within a member of this archaeal lineage (Figure 2.B) or endosymbiosis of the archaeon within a bacterium before mitochondrial symbiosis took place (Figure two.C). Therefore, if the discovery of Lokiarchaeota tin assist in refining the phylogenetic ancestry of eukaryotes, information technology also renovates quondam open questions.
Three hypothetical mechanisms to explain the evolution of the eukaryotic cell. Focus is fabricated on central eukaryotic cellular structures (nucleus, mitochondria, membrane organisation). (A) Evolution of a proto-eukaryotic lineage earlier the mitochondrial acquisition outcome; it is compatible with the classical model proposing a third primary proto-eukaryotic lineage (Figure 1.A, B) and with models proposing that the eukaryotic host derived from inside archaea (Figure i.East). (B) Endosymbiosis of mitochondrial ancestor inside i archaeon every bit the triggering upshot for eukaryogenesis (Effigy 1.C, F). (C) Endosymbiotic origin of nucleus and secondary symbiosis with ancestor of mitochondria (Figure i.D, Thou).
Open up questions on the origin of eukaryotes
Details about the more specific nature of the symbiotic partners that originated eukaryotes remain to be specified. Which are the closest living archaeal relatives of eukaryotes? Many deep-branching archaeal lineages other than the Lokiarchaeota be that might comprise more eukaryotic-similar genes [9]. What are these archaea like? Do they have eukaryotic-like features (actin cytoskeleton, vesicular-trafficking and membrane-remodeling capabilities, endocytosis and/or phagocytosis) as their genome content would predict or are those genes involved in other functions? Having tiny cells and thriving in energy-challenging environments seems at odds with high cellular complexity, only only studies on Lokiarchaeota ultrastructure and biology will provide an answer.
There are as well open questions almost the nature of the alphaproteobacterial antecedent of mitochondria. The parasitic Rickettsiales or the free-living Pelagibacter/SAR11 group accept been proposed as closest relatives to mitochondria, only recent phylogenomic analyses with improved sequence evolution models suggest that those results were affected past long-branch allure artifacts and compositional (high A+T content) biases, leaving the question unresolved [40].
Some models suggest the involvement of another bacterial symbiont different from the antecedent of mitochondria as host of the archaeon, which would become the hereafter nucleus [28,29], sometimes of very specific nature (e.g., myxobacteria) [xxx,31]. Was it the case and, if so, what was that bacterium similar? Phylogenomic analyses mostly show a variable contribution of dissimilar bacteria (other than alphaproteobacteria, for which phylogenetic signal is strong) to eukaryotes, which is interpreted every bit 'noise' derived from bacteria-to-eukaryote horizontal cistron transfer (HGT) and as lack of evidence for any item bacterial lineage [33]. Although this might well be the case, there are alternative explanations. First, many of the non-alphaproteobacterial genes in eukaryotes might have been acquired via the archaeal host, given that mesophilic archaeal lineages seem to have massively imported genes from bacteria [41], including the Lokiarchaeota [ix], or via the mitochondrial antecedent, every bit has been proposed for myxobacterial genes present in eukaryotes [42]. 2nd, if such a bacterial host ever existed, information technology would be extremely difficult to unveil its phylogenetic signal because i) it would imply an older outcome than the mitochondrial symbiosis, such that the phylogenetic indicate would have eroded, and ii) such bacterial host underwent a very of import functional shift, in contrast to mitochondria (which essentially conserve the energy metabolism of their gratis-living relatives) and the archaeal component (which kept the 'informational' functions).
However, as phylogenomic data improves, the more open and deeper questions do no longer chronicle to the phylogenetic origin of symbiotic partners but to the mechanisms and selective forces underlying the eukaryogenic process. We highlight four primal questions below; answering them will be crucial to constrain existing models.
What kind of metabolic symbiosis between eukaryogenic partners?
Regardless the type of eukaryogenic model considered (Figure two), metabolic interspecies interactions must have been cardinal for the development of the eukaryotic cell. These are widespread in nature, and particularly extended in anoxic environments, where specialized microorganisms are nearly often the source and/or sink of electron donors and acceptors [43,44]. Considering mitochondria are still responsible for the essential of eukaryotic cell energetics, some type of syntrophic human relationship must have been established between the ancestor of mitochondria and its host. Traditional views postulate a strict aerobic antecedent of mitochondria [45], while almost symbiogenetic models postulate a facultative aerobe, suggesting that eukaryotes commencement evolved in anoxic or microaerophilic environments [24,30,31]. The latter view would exist consistent with the depression-oxygen weather condition prevailing not just in Proterozoic (2.5-0.54 Ga) oceans [46] but also in contemporary oceanic (and freshwater) sediments, where Lokiarchaeaota and related archaeal lineages thrive [ix]. Indeed, many mitochondria across the eukaryotic tree (east.g. animals, fungi, euglenids, ciliates, algae, diatoms, foraminifera) produce ATP using electron acceptors unlike from oxygen (eastward.chiliad., nitrate, nitrite, or fumarate) [ii]. This might propose an anaerobic and metabolically versatile antecedent for mitochondria. Nevertheless, whereas the phylogeny of some mitochondrial proteins involved in anaerobic metabolism suggests common beginnings, that of others suggests HGT and secondary adaptation to anaerobiosis [47]. Having access to mitochondrial genes of a broader sampling of anaerobic protists would allow testing whether anaerobic respiration was ancestral and/or gained independently several times.
Thus, the original metabolic interaction betwixt the mitochondrial ancestor and its host remains undetermined. Lokiarchaeota might participate in syntrophic interactions involving fermentation [9,37]. If the mitochondrial host was an archaeon or an archaea-derived proto-eukaryote (Figure 2.A-B), it might have produced hydrogen and/or intermediate fermentation products. Was the mitochondrial ancestor an original sink for those metabolites? If the archaeon was an endosymbiont (Figure 2.C), the bacterial host might have been that metabolic sink. At any rate, interspecies hydrogen-transfer might accept been originally involved in the original eukaryogenic symbiosis. Hydrogen-mediated syntrophy is widespread in anoxic settings; the best known examples involving fermentative or sulfate-reducing deltaproteobacteria with, respectively, methanogenic or methanotrophic archaea [43,44]. The hydrogen and the syntrophy hypotheses converged in proposing such a metabolic interaction [48], where the archaeon was methanogenic (using H2 to reduce CO2 to CH4) and the bacterium involved in the chief symbiosis (the mitochondrial antecedent in the hydrogen hypothesis, the deltaproteobacterial host in the syntrophy hypothesis) was fermentative. Therefore, the archaeal partners were hydrogen sinks, not sources. While the possibility of a methanogenic ancestor for eukaryotes cannot exist completely ruled out (although Lokiarchaeota seem to lack methanogenesis, other deep-branching archaea might have possessed this pathway, especially if the last common archaeal ancestor was a methanogen, as some phylogenomic analyses seem to suggest [49]), this now seems unlikely. However, the mechanistic essence of the two symbiogenetic models (Figure ii.B-C) remains valid under a reversed metabolic interaction, where the archaeon is the hydrogen producer and the bacterium, the hydrogen sink. In the instance of the syntrophy hypothesis, the bacterial host might take been a sulfate-reducer (the original hypothesis indeed proposed a facultative sulfate reducer ancestral to myxobacteria [30,48]).
Mitochondria: early or late?
Before the discovery of the Lokiarchaeota, symbiogenetic models proposing a straight endosymbiosis of the mitochondrial ancestor within one archaeon had gained popularity [24,26,l] (Figure 2.B). They imply a triggering effect of eukaryogenesis for the mitochondrial endosymbiosis. However, the fact that the newly discovered archaea possess several homologs to membrane modeling and cytoskeleton-related eukaryotic proteins has opened the possibility for a proto-eukaryotic lineage endowed with phagocytosis to evolve from within archaea, which seems the currently favored hypothesis [nine,10]. In this case, mitochondria would contain later (Figure 2.A). The difference between the 2 situations is far from irrelevant because the driving forces underlying eukaryogenesis and the predictions of the ii models are very different. In the onetime case, the mitochondrial symbiosis would be the crusade 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 be is existent. In models invoking a bacterial host for the archaeon (Figure 2.C), the mitochondrial symbiosis is a second, independent outcome; mitochondria would therefore come later but, every bit in the case of autogenous models, the fourth dimension between the beginning of eukaryogenesis and the mitochondrial stabilization is difficult to decide. The strong alphaproteobacterial signal in eukaryotic genomes [33,51] would rather advise a relatively tardily mitochondrial incorporation upshot.
Which selective forces for the evolution of the nucleus?
The origin of the nucleus remains mysterious. While it was present in LECA and evolved equally part of the endomembrane system involving many protein components of archaeal and bacterial beginnings [52], most models do not provide any (or whatever disarming) selective forcefulness for the evolution of this defining character. Ii driving forces have been evoked past autogenous models. Condescending-Smith proposed that the nucleus evolved to prevent DNA harm caused by cytoskeletal pulling [53], an idea adopted past others [26]. Nevertheless, eukaryotic chromosomes are able to overcome mechanical stresses during mitosis, when the nuclear envelope disintegrates in many protists, even in species where chromosomes are permanently uncondensed. In addition, eukaryotes (as do prokaryotes) take efficient Deoxyribonucleic acid repair systems to cope with single and double-strand breaks occurring during the mechanically-challenging DNA-dependent processes (replication, transcription, recombination), and many eukaryotes take genomes with several dozens of chromosomes, which reduces the individual size of Deoxyribonucleic acid molecules, diminishing breakage probability. Jékely 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 accept been more than simply accomplished by retaining the ribosomal protein genes in the mitochondrial genome, as is the case with the ribosomal RNA and other protein genes for which the cytosolic synthesis and ship 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 course vesicles in the archaeal cytoplasm (Figure 2.B). The nuclear compartment would have appeared to decouple transcription and translation, thus preventing the synthesis of aberrant proteins as introns appeared [55]. All the same, 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 past the nuclear membrane must precede intron invasion. Such an idea was put forwards in the framework of the syntrophy hypothesis, which proposes the endosymbiotic origin of the nucleus [31] (Effigy 2.C). Endosymbiotic models for the origin of the nucleus easily account for the presence of a unlike compartment [21,28,31], but the difficulty here lies in how to explain what drives the endosymbiosis and the origin of the endomembrane organisation. In the syntrophy hypothesis, the endoplasmic reticulum and the nuclear membrane evolve with a chief secretory office from the internalization of the inner plasma membrane of the host bacterium, and in a fashion that is analogous to that proposed by autogenous models (and that would be almost like to the membrane internalization seen in other Gram negative leaner, with the external membrane retaining its jail cell-boundary function). This endomembrane organization would secure the distribution of hydrolytic enzymes synthesized by the archaeon towards the periplasm which, progressively, would be internalized in form of hydrolysis-related vesicles (lysosomes, peroxisomes). The formation of a proto-nuclear membrane to which ribosomes attached to deliver their products would have immune intron expansion. Once ribosomes migrated out towards the cytoplasm (interestingly, ribosomal subunits are still assembled in the nucleus), with attachment to the endoplasmic reticulum, the proto-nuclear membrane was exapted to prevent the synthesis of aberrant proteins [31]. Though these explanations seem plausible, this hypothesis is not without problems. First, endosymbiotic origins for the nucleus are often disregarded as less parsimonious than models involving only two symbionts, despite the fact that dual and multiple symbioses are frequent in natural environments [56]. Second, the transition from archaeal endosymbiont to nucleus involves the loss of the archaeal membrane and related mechanistic shifts that are hard to explain.
How did the bacterial-like eukaryotic membranes evolve?
Archaeal membranes are radically unlike from bacterial and eukaryotic membranes, having phospholipids of different composition and stereochemistry [57]. If currently favored models based on an archaea-derived host are correct, they entail a transition from archaeal to bacterial membranes (Effigy 2.A-B). However, this poses two challenges. Showtime, the plasma membrane is not only a lipid bilayer but a dynamic prison cell-environment interface, and then that the driving force leading to such transition from an already optimized system is obscure. 2d, it has been proposed that a alter of membrane composition would be viable because mixed liposomes of archaeal and bacterial lipids are stable [8]. Still, while this argument might apply to archaic, not even so optimized membranes, such as those of the concluding common ancestor [57], it is more unrealistic for circuitous membranes harboring many transmembrane proteins, which are specifically adapted to their lipid surround [58]. A alter in membrane phospholipids must therefore exist accompanied by a pervasive change in membrane proteins. Is that major shift possible? While at that place is no direct evidence for an archaea-to-bacteria membrane transition, that possibility cannot be completely ruled out. Indeed, recent studies show that mesophilic archaeal lineages for which genomic data are available take undergone extensive and convergent HGT from bacteria. Several of those convergently acquired genes relate to fatty acid biosynthesis and membrane-associated electron transfer carriers and transporters [41]. However, even if of import lineages of mesophilic archaea (e.g. haloarchaea, marine Thaumarchaeota and Euryarchaeota, mesophilic methanogens) have imported bacterial fatty acrid genes, their fate in the jail cell is uncertain since their membrane lipids remain typically archaeal (eastward.g. tetraether lipids) and based on isoprenoid moieties and glycerol-1 (instead of 3)-phosphate [59,60]. Therefore, in the absence of appreciable transitional membrane stages, the archaea-to-bacteria membrane shift remains the Achilles' heel for these models. Models proposing an archaeal endosymbiont (Effigy 2C) within a bacterial host offer, by contrast, a straightforward explanation for the bacterial-like nature of eukaryotic membranes.
Conclusions
The long-inscrutable quest for the origin of the eukaryotic prison cell has get increasingly tractable with recent progress in genome sequencing, phylogenomic analyses and the exploration of microbial diversity in natural ecosystems. The discovery of new lineages of uncultured archaea in anoxic sediments that appear more related to eukaryotes than other archaea constrains existing models for the origin of eukaryotes. However, if the prokaryotic ancestry of eukaryotes begins to be refined, cardinal questions on the eukaryogenic process remain fully open. Among them are the number and type of metabolic symbioses at the origin of the eukaryotic cell, whether mitochondria evolved early on or late and, most critically, how and why the nucleus evolved, and how the eukaryotic membrane lipids came to be (see Outstanding Questions). The devil is in the detail; thus the elaboration of detailed, plausible and, if possible, testable mechanistic models bookkeeping for all eukaryotic features is necessary to constrain existing models and unravel the transition to eukaryotic complexity.
Acknowledgements
We apologize for not being able to cite the piece of work of many authors due to space limitations. We acknowledge funding from the European Inquiry Council under the European Wedlock's Seventh Framework Plan ERC Grant Agreement 322669 'ProtistWorld'.
Glossary
| Alphaproteobacteria | highly diversified and metabolically versatile grade of bacteria within the phylum Proteobacteria from which the antecedent of mitochondria evolved. |
| Archaea | one of the iii classically recognized domains of life and one of the two primary phylogenetic domains. Archaea exhibit prokaryotic prison cell structure. They are traditionally divided in two main branches, the Euryarchaeota and the TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) superphylum or Proteoarchaeota. |
| Autogenous models | hypotheses postulating that the endomembrane system and the nucleus upshot from the invagination of the plasma membrane in a proto-eukaryotic or a prokaryotic ancestor. Historically, before the general acceptance of the endosymbiotic origin of mitochondria and chloroplasts, the term too referred to the internal development of these organelles from endogenous endomembranes. |
| Deltaproteobacteria | proteobacterial class encompassing predominantly anaerobic, sulfate-reducing bacteria, fermentative syntrophic leaner (east.k. Syntrophomonas) and myxobacteria. |
| Endosymbiosis | symbiotic relationship in which one partner (endosymbiont) is inside the other (host). |
| Endosymbiotic gene transfer | transfer of genes from the genome of the endosymbiont to that of the host; in some cases it can lead to consummate genome extinction. |
| Eocyte | term historically applied to the archaeal clade that was more like to eukaryotes based on ribosomal proteins (originally, the Crenarchaeota); by extension, some authors apply information technology today to the TACK superphylum. |
| Eukaryogenesis | process that led to the evolution of the eukaryotic prison cell from prokaryotic ancestors. |
| Hydrogenosome | hydrogen-producing organelle that evolved from mitochondria. |
| Mitosome | a type of MRO, genome-defective simple mitochondrial remnant where Atomic number 26-South clusters are assembled. |
| MRO | mitochondria-related organelle; includes hydrogenosomes, mitosomes and, in general, organelles derived from mitochondria. |
| Mutualism | symbiosis beneficial for the interacting partners. |
| Myxobacteria | too known as 'slime' or 'social' bacteria, group of Deltaproteobacteria characterized by complex genomes, gliding movement, coordinated multicellularity and prison cell differentiation. |
| Neomura | hypothetic clade composed past Archaea + Eucarya that would have evolved from single-membrane-bound, Gram-positive bacteria. |
| Planctomycetes | bacterial phylum containing some members with more-or-less developed endomembrane systems that sometimes resemble nuclear-like membranes (eastward.chiliad., Gemmata obscuriglobus). |
| Phylogenomics | molecular phylogenetic analyses of genome-derived information. |
| Serial endosymbiotic theory | evolutionary eukaryogenic scenario proposed by Lynn Margulis stating that mitochondria and chloroplasts derived from endosymbiotic bacteria subsequent to merging symbiosis between a wall-less archaeon and motility-providing spirochetes. |
| Symbiogenesis | evolutionary procedure mediated past symbiosis at the origin of the eukaryotic jail cell. |
| Symbiosis | intimate and durable inter-species interaction; generally practical to parasitic, mutualistic and commensal interactions, only sometimes applied more than restrictively to mutualism. |
| Syntrophy | symbiosis mediated past metabolic interactions. |
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Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640172/
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