The Evolution of the Three Domains
Phylogeny refers to the evolutionary relationships between organisms. The three domains are the Archaea, the Bacteria, and the Eukarya. and complex webs of genetic relationships among the three evolving lineages. of many different species from the domains Bacteria, Archaea, and Eukarya. Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya. Thomas L(1).
- 1.3: Classification - The Three Domain System
- The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
Because rRNA molecules throughout nature carry out the same function, their structure changes very little over time. Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good indication of how related or unrelated different cells and organisms are. There are various hypotheses as to the origin of prokaryotic and eukaryotic cells. Because all cells are similar in nature, it is generally thought that all cells came from a common ancestor cell termed the last universal common ancestor LUCA.
These LUCAs eventually evolved into three different cell types, each representing a domain. The three domains are the Archaea, the Bacteria, and the Eukarya.
A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryota domains. More recently various fusion hypotheses have begun to dominate the literature.
One proposes that the diploid or 2N nature of the eukaryotic genome occurred after the fusion of two haploid or 1N prokaryotic cells.
Others propose that the domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor that itself emerged from a member of the domain Bacteria. Some of the evidence behind this hypothesis is based on a "superphylum" of bacteria called PVC, members of which share some characteristics with both archaea and eukaryotes. There is growing evidence that eukaryotes may have originated within a subset of archaea. In any event, it is accepted today that there are three distinct domains of organisms in nature: Bacteria, Archaea, and Eukarya.
A description of the three domains follows. There is a "superphylum" of bacteria called PVC, referring to the three members of that superphylum: Some of these bacteria show cell compartmentalization wherein membranes surround portions of the cell interior, such as groups of ribosomes or DNA, similar to eukaryotic cells.
Some divide by budding or contain sterols in their membranes, again similar to eukaryotes. Some lack peptidoglycansimilar to eukaryotes and archaea. It has been surmised that these bacteria migh be an intermediate step between an ancestor that emerged from a bacterium domain Bacteria and an archael-eukaryotic ancestor prior to its split into the domains Archaea and Eukarya.
Electron micrograph of the bacterium Gemmata obscuriglobus, a planctomycete noted for its highly complex membrane morphology, illustrating representative morphologies. PLoS Biol 8 1: Archaea are prokaryotic cells. The cell walls of Archaea contain no peptidoglycan. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya.
Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. One reason for this is that the ether-containing linkages in the Archaea membranes is more stabile than the ester-containing linkages in the Bacteria and Eukarya and are better able to withstand higher temperatures and stronger acid concentrations.
The Bacteria eubacteria Bacteria also known as eubacteria or "true bacteria" are prokaryotic cells that are common in human daily life, encounter many more times than the archaebacteria. Eubacteria can be found almost everywhere and kill thousands upon thousands of people each year, but also serve as antibiotics producers and food digesters in our stomachs. The Bacteria possess the following characteristics: Bacteria are prokaryotic cells. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.
Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya. Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria. The Eukarya eukaryotes The Eukarya also spelled Eucarya possess the following characteristics: Eukarya have eukaryotic cells.
Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan. This remains true even if a few ex-ESPs e.
What is the evolutionary relationship among Archaea, Bacteria, and Eukarya?
The number, diversity, and complexity of ESFs are impressive and their origin remains a major evolutionary puzzle that should not be underestimated. The puzzle became of even greater magnitude when it was realized during the last decade from phylogenomic analyses that all ESFs and associated ESPs were most likely already present in the last common ancestor of all modern eukaryotes, the last eukaryotic common ancestor LECA [ 20 ]. Besides lacking by definition all ESFs, archaea also fundamentally differ from eukarya in the nature of their membranes with a unique type of lipids in archaeaand the type of viruses infecting them.
The problems raised by the evolution of membranes have been nicely reviewed recently by Lombard et al. 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. Another Evolutionary Puzzle Viruses infecting archaea have fascinated for a long time scientists that are aware of their existence by the amazing morphologies of their virions that, in most cases, differ drastically from those produced by bacterioviruses formerly bacteriophages or eukaryoviruses [ 2425 ].
Among the 13—15 families of archeoviruses presently known, most are unique to archaea, and none of them is specifically related to a family of eukaryoviruses. The only archaeal viruses with eukaryovirus relatives are the archeoviruses STIV Sulfolobus islandicus turreted virus see below and Caudovirales, which belong to major lineages of viruses infecting members from the three cellular domains [ 26 ].The Three Domains of Life
Viruses of this lineage are characterized by major capsid proteins containing the so-called double jelly-roll fold. Archaeal and bacterial Caudovirales head and tailed viruses belong to the same viral lineage as eukaryoviruses of the family Herpesviridae. Their virions are constructed from the major capsid proteins displaying the so-called Hong-Kong 97 fold structurally unrelated to the jelly-roll fold. Strikingly, the archaeal viruses in these two lineages are much more similar in virion size and overall structure to their bacterial than to their eukaryotic counterparts.
In particular, archaeal and bacterial Caudovirales are identical in terms of virion morphology and genome organization and share several homologous proteins [ 27 ]. The three families of Caudovirales Siphoviridae, Myoviridae, and Podoviridae first described in bacteria have been now found in archaea [ 252728 ].
Classification - The Three Domain System - Biology LibreTexts
Moreover, Caudovirales were recently found to be more widespread than previously thought among archaea, suggesting that Caudovirales already existed when archaea and bacteria started to diverge from each other [ 29 ]. Finally, a recently described family of archaeal pleomorphic viruses, pleolipoviruses, could be related to bacterial pleomorphic viruses of the family Plasmaviridae [ 30 ].
In summary, whereas archaea and eukarya share basic molecular biology features for all major ancestral cellular functions, the archaeal virosphere shares much more similarities with the bacterial one than with the eukaryotic one.
Beside common viruses, archaea and bacteria also share similar types of plasmids, insertion sequences ISand related transposons [ 2527 — 35 ]. Furthermore, they detected no IS elements in archaeal genomes with significant similarity to the nine known superfamilies of eukaryotic DNA transposons [ 31 ].
Plasmids are abundant, diverse in size, and widespread in archaea, as in bacteria, contrasting with the paucity of plasmids in eukaryotes. Moreover, archaeal ISs and plasmids use bacterial-like proteins for transposition, plasmid resolution, and segregation [ 31 ].
Some of these proteins are only present in archaea and bacteria, and when they are universal for instance initiator proteins for rolling circle replication the archaeal version is more similar to the bacterial version than to the eukaryotic one [ 3637 ]. The bacterial affinity of archaeal viruses and plasmids confirms that these mobile elements are evolutionarily related, with plasmids probably being derived from ancient viral lineages [ 38 ].
This would fit with a provocative scenario in which I suggested that the archaeal and bacterial chromosomes evolved from large DNA plasmids, with divergent replication mechanisms but homologous partition machineries, themselves derived from giant DNA viruses [ 40 ]. Finally, it is striking that archaea and bacteria use homologous defence systems against plasmids and viruses CRISPR, toxin-antitoxin and restriction-modification systems that are very divergent from the siRNA interference defence systems used by eukaryotes [ 4142 ].
Homologues of argonaute proteins, the core component of the eukaryotic interference system, have been detected in archaea and bacteria, but it is not yet known if these proteins are involved in an interference pathway [ 4243 ]. All these observations raise major unresolved questions: Why, on the other hand, so many viruses infecting archaea are unique, having neither bacterial nor eukaryotic counterparts?
A good theory for the origin of archaea and their relationships with eukarya should definitely explain these puzzling observations.