Origins of Eukaryotes: Who are our closest relatives? - Science in the News
Woese and Fox's paper on the discovery of the Archaea triggered a comprise two distinct types of organisms, the Bacteria and the Archaea. the precise evolutionary relationship between eukaryotes and archaea has. The domains are Archaea, Bacteria, and Eukarya. The kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista. a | In the 'three primary domains' (3D) scenario, the Eukarya, Archaea and Bacteria form three primary domains, each with a specific most.
We argue that the PVC features represent intermediate steps between the three domains and that the presence of such features in a bacterial superphylum suggests a scenario in which the ancestor of the current PVC members was related to the LAECA.
This in turns supports that the eukaryotic endomembrane system evolved by internalization of the bacterial periplasm. The PVCs are consistently recovered as a monophyletic group in phylogenetic trees based on a variety of methods and datasets, but those analyses are inconclusive as to the relationship of PVC members with the other bacterial groups [ 11 — 25 ].
Challenges posed by the compartmentalization of planctomycetes have been outlined [ 26 ]. Eukaryotic and archaeal features in Planctomycetes, Verrucomicrobiae and Chlamydiae members The similarities between PVC members that lend support to the monophyly of the group include features that are uncommon for bacteria and usually considered as eukaryote- or archaea-specific.
These features are summarized below note that not all features are found in all PVC members. This is ultimately demonstrated by the fact that, like in other bacteria, ribosomes line up against the inner membrane and, in PVC members, its invaginations. This feature is shared between PVC members but shows important variations [ 2830 ].
In the planctomycete Gemmata obscuriglobus, the invaginations and derived membrane morphologies appear to be dynamic and cell cycle-dependent [ 29 ]. The presence of this feature in most PVC members suggests that the ancestor of the PVC supergroup already had this feature [ 28 ].
In addition, it has been claimed that the G. It is, however, unclear whether this membrane completely surrounds the DNA and detailed three-dimensional studies of this planctomycete are needed to solve this important issue. Membrane coats MCs are proteins that play key roles in shaping eukaryotic membranes.
Most MCs exhibit a unique arrangement of beta-propeller and alpha-helical repeat domains [ 32 ] thought to be exclusive to eukaryotes until their discovery in various PVC members [ 29 ]. In addition, MCs have been associated with membrane manipulation and endocytosis see below in the planctomycete G.
No signs of a recent horizontal gene transfer HGT to or from the bacteria could be detected leading to the suggestion that the bacterial PVC superphylum contributed to the origin of the eukaryotic endomembrane [ 29 ]. A more complete characterization of the proteins involved in the definition of the PVC endomembrane system would bring important answers.
Like the eukaryotic genomic material, the nucleoids in PVC members appear condensed when cryofixed and cryosubstituted [ 2728 ] which, unlike conventional chemical fixation, is not expected to yield such condensation as an artefact.
This contrasts with the appearance of cryofixed nucleoids from other bacterial species such as Escherichia coli and Bacillus subtilis, where an irregularly shaped nucleoid extends through the cell cytoplasm. Several proteins related to eukaryotic chromatin-associated ones are present in the Chlamydia trachomatis genome, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and decondensation [ 33 ]. Chlamydiae are also one of the few prokaryotic organisms reported to contain proteins homologous to eukaryotic histone H1, although the similarity might be biased by the low complexity of the protein [ 34 — 36 ].
However, owing to their parasitic lifestyle, the possibility of HGT is difficult to rule out. Planctomycetes are one of the few groups of bacteria that reproduce by budding [ 38 ]—a mode of division more commonly associated with eukaryotes.
Sterols and related compounds play essential roles in the physiology of eukaryotic organisms, including the regulation of membrane fluidity and permeability. Sterols are almost completely absent in prokaryotes but are nearly ubiquitous in eukaryotes.
The origin of sterol biosynthesis is still debated but it is accepted that the early eukaryote could synthesize a large array of different sterols [ 39 ]. Among the few bacteria that synthesize sterol, G. The primitive sterols suggest that this genus has retained an ancient sterol biosynthetic pathway.
Archaea and the origin of eukaryotes.
No evidence of HGT was found in planctomycetes. A definitive phylogenetic analysis of the PVC sterol synthesis pathway would bring invaluable clues to this important process. The membranes of planctomycetes contain lipids that are more typical of eukaryotes, such as palmitic, oleic and palmitoleic lipids [ 41 ]. One of the distinguishing features of archaea is the presence of ether-linked lipids rather than the ester-linked lipids found in bacteria. Eukaryotes contain both types of lipid.
How these lipid pathways evolved is a fundamental question in biology [ 4243 ]. Anammox planctomycetes have a variety of unusual lipids, and are the only prokaryotes having both ether- and ester-linked lipids in their membranes, and could thus be considered a transition point for this feature between archaea and bacteria [ 44 ]. Determining the cellular localization of the different lipid classes and how they coexist would have tremendous evolutionary implications.
C1 transfer chemistry is at the core of two important reactions central to the Earth's methane balance, methanotrophy and methanogenesis. The origins of both are still unknown. Methanotrophs are mainly found in the alpha- beta- and gamma-proteobacteria as well as in some archaea and methanogens in the archaeal domain Euryarchaeota.
Planctomycetes have also been shown to contain C1 transfer genes [ 4546 ]. Ancient divergence of Verrucomicrobia and Proteobacteria C1 genes has been recognized [ 47 ] but their phylogenetic position is still disputed [ 454648 ]. Determining the enzymatic activity of the PVC C1 enzymes would be revealing in this respect.
Peptidoglycan is a standard component of almost all bacterial cell walls but is absent from the cell walls present in many eukaryotes and archaea. The peptidoglycan synthesis genes are contained in the division and cell wall dcw gene cluster that is highly conserved in bacteria.
However, the dcw gene cluster shows alteration in most PVC members and is almost completely absent in some of them [ 16 ]. In addition, the cell wall of various Planctomycetes, like eukaryotes, is mainly composed of proteins [ 41 ]. Bacterial cell division relies on concentric rings of the FtsZ protein.
FtsZ is found in most bacteria and in one subdivision of the archaea, the Euryarchaeota, whereas its homologue, the cytoskeleton protein tubulin, is usually restricted to eukaryotes. Unlike most bacteria, some PVC members show alteration of the ftsZ gene, while it is absent in Chlamydiae and Planctomycetes [ 1625 ].
Some Verrucomicrobia have both tubulin and FtsZ homologues encoded in their genome; a situation unique among all forms of life [ 49 — 51 ].
It is not clear if the presence of tubulin in this bacterium is the result of HGT or of a deep evolutionary connection. However, the Verrucomicrobia tubulins do not branch within the eukaryotic ones in phylogenetic trees, but instead behave as an outgroup, arguing against HGT from a modern eukaryote [ 49 ]. In addition, the Prosthecobacter genes represent an intermediate step between FtsZ and tubulin, in terms of both structure and folding [ 51 — 54 ].
One clue to understand those unique PVC features is that the essentiality of the ftsZ gene is most probably linked to the presence of a peptidoglycan cell wall [ 55 — 58 ]. Key to eukaryotic evolution was the development of endocytosis, the process by which cells absorb molecules such as proteins from outside the cell by engulfing them with their cell membrane. Phylogenetic analysis suggests that the endocytic molecular machinery must have been present in the last eukaryotic common ancestor LECA [ 59 ].
Unexpectedly, a related process has now been described in the planctomycete G. This process is linked to MC-like proteins, and is energy-dependent and receptor-mediated, rendering it similar to eukaryotic endocytosis.
Determining the players involved in this process would thus be extremely important. The last PVC common ancestor. The presence of the above characteristics in a diffuse pattern throughout the members of the PVC superphylum suggests that the LPCA had most of these features and some were subsequently lost during divergence of the phyla. Other bacteria with eukaryotic or archaeal features.
PVC superphylum members are not the only bacteria to display archaeal- or eukaryotic-like features. For example, the endomembrane vesicles found in Rhodobacter are mostly protein dominated [ 61 ] and not sustained by MC-like proteins, like those found in PVC members. In addition, the PVC superphylum is the only one combining so many of these features in related species. Evaluating the evolutionary relationship of these particular bacterial features is a difficult task owing to the dominant lack of sequence similarity between PVC proteins and their non-bacterial counterparts.Overview of Archaea, Protista, and Bacteria - Cells - MCAT - Khan Academy
The paucity of sequence information raises the possibility that any similarities observed may be the result of misinterpretation or, at best, convergence. If so, a thorough characterization of the PVC features will still provide invaluable insight into the alternative development of those features.
Transitional forms between the three domains of life and evolutionary implications
Although HGT can be invoked on a case-by-case basis, a global view argues against such considerations. Firstly, this possibility has been investigated in several cases, i. While the three-domains hypothesis implies that Archaea and Eukarya had a common ancestor, which then split into the two lineages, the archaeal-host hypothesis implies that the first Eukaryotes arose directly from an Archaea. In other words, this means that the first Eukaryote was probably an Archaea that somehow acquired the cell structure present today only in Eukarya, perhaps by fusion with another cell.
The implication of this alternative hypothesis is that we are members of the Archaea domain, and that there are only two, not three, domains of life.
A sister-group relationship is indicated by a branch that splits into the two groups. It means that these groups share a more recent common ancestor with each other than with any other group in the tree and therefore are more closely related.
Modified with permission from  Macmillan Publishers Ltd: Reconstructing the ancient history of life Inferring the phylogeny of a group can be done by following a few steps: By comparing the same parts of the sequence across all species, we can conclude that the more similar they are, the closer those organisms are historically.
This seems straightforward, but in fact it is not. Having a good sampling of the diversity of organisms is very important because it is hard to account for information that is unknown, so there is a risk of getting the history wrong if just a few species are represented.
Archaeal samples have been especially underrepresented, since they often occupy extreme environments and are hard to cultivate in the lab. However, recent advances in molecular methods now allow us to obtain sequences directly from organisms in natural environments. These new data support the archaeal-host hypothesis and find that the closest relatives of the Eukaryotes are one or all of the TACK Archaea  Figure 2b.
Different models of sequence evolution also have a large impact on the outcome of phylogenetic analyses. Simple models of evolution generally assume that all the DNA positions in a sequence evolve at the same rate, and that base composition A, C, G, T in the DNA is constant across different groups.
Analyses using those models traditionally recover the three-domains tree. However, those simplified assumptions are not justified in most cases. Base frequencies actually vary widely among the three domains, and more complex models that take this into account need to be used to avoid error.
Also, there are sites that go through base changes more often, while others are constrained by natural selection and remain the same for longer periods of time — for instance when changes in certain regions of the DNA are more likely to damage its function than changes in other positions, so that variations in the former will often be selected against.
To deal with such issues, different models of evolution can be applied to different parts of sequences, and more sophisticated models have recently supported the archaeal-host hypothesis [5, 6].
Another issue comes from the disagreement among genes: Important genes to be considered in phylogenetic reconstruction of such ancient relationships are those that are very conserved, meaning that they are very similar in long-diverged species.
Long periods of time make possible the occurrence of consecutive changes in the same site, which confuses the analysis. Some genes, however, are very important in the integration of cell functions and thus are very constrained by selection. Examples are sequences related to transcription and translation reading genes and transforming their code into proteins, respectively.
Eukaryotic genomes are a mixture of genes from distinct origins. Some are very similar to bacterial genes because they indeed have a bacterial origin. They were transferred to Eukaryotes from the bacterium that was engulfed by an early Eukaryote and eventually became the mitochondria organelle responsible for energy production inside cells .
But after comparing the similarity in conserved genes among the Bacteria, Archaea and Eukarya, studies found that they were more similar between Eukarya and subgroups of Archaea TACK. This supports the archaeal-host hypothesis , in which important genes in the nucleus came from the host that gave rise to the Eukaryotic lineage. Controversy Even with great support for the archaeal-host tree, we are still missing parts of the story. For example, a major challenge to the hypothesis is to explain the evolution of the membrane that surrounds cells.
Membranes in Bacteria and Eukarya have the same biochemical structure, while Archaea have a different type . Following the tree, the first membrane to exist was the one from Bacteria, which then went through modifications in the Archaea lineage.
If, as in the three-domains hypothesis, Eukarya was an independent lineage from Archaea, this would mean that Eukaryotes kept the original membrane and that the new one appeared in Archaea.