What is the difference between archaea and eukarya

There are many examples in the evolution of modern eukaryotes that testify for the importance of viral proteins in the evolution of eukaryotes. For instance, exaptation of a retroviral protein, syncytin, has been critical for the formation of placenta in mammals [ ].

These phenomena also occur in archaea and bacteria, but considering the extreme abundance of mobile elements in eukaryotic genomes, their importance in eukaryotes is an order of magnitude higher. The integration of ancient Megavirales can also explain why the eukaryotic core genomes contain many bacterial genes of different origin and without affinity to the mitochondrial alpha-proteobacterium ancestor.

These bacterial genes are usually supposed by proponents of fusion hypotheses to derive from the bacterial partner [ — ]. I suggest here that many of these genes have not been directly transferred from bacteria to protoeukaryotes but that these transfers have been mediated by ancient Megavirales. Megavirales with linear genomes have probably recruited these genes from endosymbiotic bacteria living in their hosts via their specific DNA replication mechanism [ ].

Eukaryotes might have also recruited their messenger RNA capping system from ancient Megavirales [ ], since these viruses use for capping the eukaryotic system, whereas other lineages of viruses use different systems [ ]. The viral diversity in terms of capping mechanisms suggests that different capping mechanisms originated several times independently in the viral world and that one of them was transferred later on into the protoeukaryotic lineage [ ].

The idea to tag chemically its own messenger RNA to discriminate it from the messenger RNA of your host can be viewed as a typical viral trick that was later on stolen by eukarya in the arms race between viruses and cells. Besides, megavirales, retroviruses, retroelements, and other eukaryotic transposons have been probably a major source of variations at the origin of eukaryote evolution [ 46 , 74 ]. These genetic elements, which represent a large portion of modern eukaryotic genomes, have been critical factors in recent eukaryotic evolution [ ].

The mobility of IS triggers rapid genome rearrangements and modifies genome expression patterns, providing new promoter elements, activating or regulating genes, even creating new genes by interfering with alternative splicing.

It is therefore tempting to suggest that retroviruses have been used as toolkits in the formation of some ESFs at the onset of the eukaryotic lineage. Indeed, telomeres are evolutionarily related to retroposons of the Penelope family [ , ] and telomerases are homologous to reverse transcriptases [ ].

Moreover, centromeres are formed by the repetition of numerous retroelements [ ]. The cell nucleus itself might have originated as a protective device allowing the cell to hide their chromosomes from viruses [ 46 , , ]. For this purpose, cells might have recruited viral proteins able to manipulate the endoplasmic reticulum membranes, and that were originally used to build viral factories [ ].

This scenario is supported by the fact that viruses themselves use viral factories to protect their replication machinery from the defence systems of the host [ ]. I have previously emphasized the profound difference existing between the eukaryotic defence mechanisms against viruses and those used in common by archaea and bacteria.

The arms race between eukaryotes and their specific viruses or else the necessity for eukaryotic cells to somehow control the spread of their specific transposons probably played an immense role in the specific evolution of the eukaryotic cells. It is clear for instance that exaptation of the siRNA antiviral defence system by eukarya to produce various types of microRNA has been decisive in the evolution of eukaryotic cells toward complexity.

Modern eukaryotes use DNA methylation and histone modifications to limit the spread of mobile elements [ ]. It is possible that these mechanisms that are typical of eukaryotic cells first originated as tools in the arms race between eukaryotes and their viruses and were recruited only later on for gene regulation in eukaryotes. Interestingly, these megavirales and retroviruses are also unknown in yeasts.

The absence of the siRNA antiviral defence system in archaea and bacteria is also remarkable. If we agree that LAECA was more complex than archaea and less complex than eukarya, the main question now is how much was it more and less complex than archaea and eukarya, respectively?

To counterbalance, I will try to push somewhat in the other direction. It is now often assumed for instance that the spliceosome machinery of eukarya derived from group II introns present in the mitochondrial ancestor or in ancient endosymbiotic bacteria, because some RNA components of the spliceosomes are evolutionarily related to group II introns [ 67 , 68 , ].

However, this does not explain why intermediates of this evolutionary process have never been observed, despite the fact that eukaryotes have continued to coexist after LECA for billion years with intracellular bacteria harbouring group II introns. Moreover, comparative genomics analyses have shown that the LECA had a spliceosome and contained probably a plethora of spliceosomal introns [ 94 ] and it seems unlikely that such incredibly complex molecular machine could have emerged in a short time between the FME and LECA.

Interestingly, it has been shown recently that the genomes of some nucleomorphs have lost all introns and all genes encoding components of the spliceosomal machinery [ ]. The nucleomorphs are remnants of eukaryotic nucleus from eukaryotic endosymbionts that are present in some photosynthetic protists. This observation tells us that the spliceosome and protein coding genes containing introns could be in fact an ancestral feature that was completely lost in bacteria and eukarya, while being retained in eukarya.

This scenario would make sense since the spliceosome machinery a giant ribozyme reminds strikingly the ribosome, suggesting that both are remnants of the RNA world. Kurland et al. This would imply the presence of an already quite elaborated cytoskeleton in LAECA, with possibly already an endoplasmic reticulum. I have no space here to discuss the timing of appearance of the modern eukaryotic nucleus with typical eukaryotic chromosomes, mitosis and meiosis, and so on.

Is it possible or not for a specific ancestral ESF, once established, to have completely disappeared in archaea and bacteria? The nucleomorph story tells us that the answer is yes for the spliceosome. Beside intellectual constructions, we should look for similar examples to try obtaining answers for other ESFs. A major question whose answer could help us to go further in our scenario is, what kind of viruses infected LAECA?

If viruses are very ancient, as now suspected, having emerged well before LUCA [ 26 , , ], the logical conclusion would be that LAECA and closely related organisms living at that time were infected by ancestors of all viruses infecting now archaea and eukaryotes. This would mean that protoretroviruses and protomegavirales were around at that time and have been later on lost in the archaeal lineage.

If true, as previously discussed, this might have maintained this lineage irreversibly into the path of reduction. Major questions then remain to be tackled such as, why so many lineages of archaeal viruses, such as Fuselloviridae, Rudiviridae, Lipothrixviridae, Clavaviridae, and so on, have disappeared in eukarya?

One possibility may be that invention of the nucleus dramatically reduced the number of viral families capable to survive this invention, because, originally, only a few viruses were able to replicate in the cytoplasm.

This system was possibly more specific to those viruses that were lost in eukaryotes? Similarly, one can wonder why archaea lost the siRNA interference system? Interestingly, many viral families known in Crenarchaeota, such as Rudiviridae, Lipothrixviridae, and Clavaviridae, are presently unknown in Euryarchaeota.

It seems unlikely that these viruses originated de novo , in the branch leading to Crenarchaeota. If these viruses were present at the time of LACA, this implies that these vital families were eliminated in the lineage leading to Euryarchaeota. If this is the case much more work on archaeal viruses will be required to confirm this scenario this could indicate that loss of viral lineages is indeed a common feature in the emergence of novel cellular lineages.

These previous observations remain valid but let open the resolution of the rooting problem itself. For example, nonhomologous archaeal eukaryal and bacterial ribosomal proteins or transcription factors often occupy the same site on the ribosome and RNA polymerase, respectively, and it is difficult to imagine how one set of proteins was replaced by the other. However, two more recent findings suggest that LAECA already had a DNA genome: 1 the discovery in Thaumarchaeota of a type IB DNA topoisomerase that was probably present in LAECA [ 19 ] and 2 the observation of conserved genomic contexts in archaea suggesting the existence of a regulatory mechanism coupling DNA replication and translation conserved between archaea and eukarya [ ].

If the universal tree is indeed rooted in the bacterial branch, this implies LUCA being a mesophile that adaptation to thermophily has occurred twice independently, once in the branch leading to archaea and once in the branch leading to bacteria Figure 3. I wonder if the fact that archaea and bacteria experienced similar selection pressure at their origin adaptation to high temperature could explain why they share partly similar types of mobile elements? In the case of bacteria, an important event in the formation of this lineage was the invention of peptidoglycan and thick cell walls.

The wide distribution of genes involved in the biosynthesis of peptidoglycan in bacterial genomes [ ] suggests that this unique structure was already present in the LBCA. This invention could have dramatically reduced the number of viral lineages effective against bacteria, allowing bacteria to escape those lineages of viruses that are now archaea specific [ — ].

The efficiency of peptidoglycan against some devices produced by archaeal viruses is well illustrated by the failure of archaeal virus-associated pyramids VAP expressed in Escherichia coli to cross the peptidoglycan [ ]. Archaeal VAP accumulate in the periplasm of E. To conclude this paper, let us have a time vision back to a population of LAECA-like organisms, relatively complex cells with internal membranes and spliced genes, infected by a myriad of diverse DNA and RNA viruses.

In that population, a particular bug has two offsprings, each of them gave rise to many lineages by binary fission. In one of these lineages, cells improved their capacity for phagocytosis, increased their size, and became first class predators the ancestors of eukaryotes. Some of them invent the nucleus and become free from many viruses that infected LAECA, except those that, in a first time, could replicate in the cytoplasm later on, some viruses will find their way to the nucleus.

To escape these big raptors [ 50 ], cells from another lineage started to reduce their size and increased their growth rate. Among their descendants, a particular lineage survives all damn big raptors living around by jumping into hot water.

In that process, they get rid of many viruses that tortured them before in particular all RNA viruses , but many viruses succeeded to follow them.

Some descendants of these first hot swimmers started to like it very hot; making use of isoprenoids, they built a new type of membrane, and, fusing a helicase and a topoisomerase, they invented an amazing enzyme, reverse gyrase, to stabilize we still do not know how their genomes [ ].

These superbugs became the only organisms capable of living at temperature near or above the boiling point of water. One of them became LACA, the last common ancestor of all modern archaea, organisms that had become so sophisticated in their way of life and physiology that they are now capable of confronting the giant descendants of the big raptors, sometimes even to live inside their guts. These fast-growing microbes also had succeeded to escape predators for a while and to get rid of many viruses previously disturbing their ancestors by inventing peptidoglycan bringing with them some viruses well known by archaea , but they have not invented a new type of membrane.

They have just adjusted their classical version to better survive in hot water. They have not invented reverse gyrase, but many of them will capture this amazing enzyme from archaea to thrive happily in hot water [ ]. However, bacteria have invented another enzyme, DNA gyrase, which provides them with a dramatic selective advantage by coupling gene expression rapidly to environmental fluctuations via supercoiling-dependent modification of promoter activities [ ].

However, archaea will survive this bacterial expansion and expand themselves out of their initial hot cradle. Taking benefit of their unique lipids, they will thrive in energy poor biotopes, deep in the ocean, or in soils and lakes with low oxygen content [ ]. Later on, catching gyrase from bacteria, some euryarchaea Haloarchaea, Archaeoglobales, Thermoplasmatales, and Methanogens will become able to confront and coexist with bacteria with equal efficiency in many different types of environments [ ].

This is only one of the drawbacks of using the term prokaryote. I agree on this point with Pace who has strongly advocated to completely repel the term prokaryote [ ]. I proposed in the same paper to rename in parallel eukaryotes by the neutral term synkaryotes with a nucleus. However, synkaryote, referring to a phenotypic trait, is not really adequate to name a domain, defined instead by genotypic traits [ 53 ].

Indeed, the origin and fate of the spliceosome s is, in my opinion, one of the more important questions in the history of life. The proposed hypotheses will possibly then seem less unorthodox to you. This paper is dedicated to the memory of Carl Woese, who has dramatically changed the life and career of so many biologists all over the world by his visionary work on microbial evolution.

The author thanks Mart Krupovic for critical reading and correction of this paper. National Center for Biotechnology Information , U. Journal List Archaea v. Published online Nov Author information Article notes Copyright and License information Disclaimer. Received Jul 22; Accepted Sep This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article has been cited by other articles in PMC. Abstract It is often assumed that eukarya originated from archaea. Introduction Archaea have been confused with bacteria, under the term prokaryotes, until their originality was finally recognized by 16S rRNA cataloguing [ 1 ]. The Bacterial Flavour of Archaeal Viruses and Plasmids: 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 [ 24 , 25 ].

Different Scenarios for the Origin of Archaea and Eukarya Several scenarios are in competition to explain the origin of archaea and eukarya [ 20 — 22 , 44 — 52 ]. Open in a separate window. Figure 1. Criticism of Fusion Scenarios I have previously proposed my own fusion scenario, as a joke [ 46 ], accompanied by criticisms against my new version of the fusion the association of a thaumarchaeon and a PVC bacterium.

The Monophyly of Archaea As previously mentioned, it is commonly assumed that the eocyte tree is now validated by phylogenetic analyses in which eukarya emerge from within archaea [ 55 , 58 — 60 ], with the consequence that all eukaryotic ESFs should have originated in a highly divergent archaeal lineage and that archaea are our ancestors.

Figure 2. Figure 3. Divergent Evolutionary Trends Shaped the History of Archaea and Eukarya We have always the tendency to interpret evolution as a general trend from simple to complex because, as Homo sapiens , we are still under the spell of the Aristotle's scala natura.

Figure 4. Figure 5. Conflict of Interests The author declares that there is no conflict of interests. Acknowledgments This paper is dedicated to the memory of Carl Woese, who has dramatically changed the life and career of so many biologists all over the world by his visionary work on microbial evolution. References 1. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Zillig W. Comparative biochemistry of Archaea and Bacteria.

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Members of this ubiquitous phylum play an important role in the fixation of carbon. Many members of this group are sulfur-dependent extremophiles. Some are thermophilic or hyperthermophilic. This group currently contains only one species: Nanoarchaeum equitans. Nanoarchaeum equitans : This species was isolated from the bottom of the Atlantic Ocean and from a hydrothermal vent at Yellowstone National Park. It is an obligate symbiont with Ignicoccus , another species of archaea.

Nanoarchaeum equitans small dark spheres are in contact with their larger host, Ignococcus. This group is considered to be one of the most primitive forms of life. Members of this phylum have only been found in the Obsidian Pool, a hot spring at Yellowstone National Park. No members of this species have been cultivated. This image shows a variety of korarchaeota species from the Obsidian Pool at Yellowstone National Park. The prokaryotic plasma membrane is a thin lipid bilayer 6 to 8 nanometers that completely surrounds the cell and separates the inside from the outside.

Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules.

In archaeal cell membranes, isoprene phytanyl chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers Figure 2. Figure 2.

Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways. First, they have branched phytanyl sidechains instead of linear ones. Second, an ether bond instead of an ester bond connects the lipid to the glycerol. The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes.

Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis bursting due to increasing volume. The chemical composition of the cell wall varies between Archaea and Bacteria, and also varies between bacterial species. Bacterial cell walls contain peptidoglycan , composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine.

Proteins normally have only L-amino acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell-wall development. There are more than different forms of peptidoglycan. S-layer surface layer proteins are also present on the outside of cell walls of both Archaea and Bacteria. Bacteria are divided into two major groups: Gram positive and Gram negative , based on their reaction to Gram staining.

Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others are Gram-negative.

The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram — The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms Figure 3.

Up to 90 percent of the cell-wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane.

Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan only 10 percent of the total cell wall , surrounded by an outer envelope containing lipopolysaccharides LPS and lipoproteins.

This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes. Bacteria are divided into two major groups: Gram positive and Gram negative. Both groups have a cell wall composed of peptidoglycan: in Gram-positive bacteria, the wall is thick, whereas in Gram-negative bacteria, the wall is thin.

In Gram-negative bacteria, the cell wall is surrounded by an outer membrane that contains lipopolysaccharides and lipoproteins. Porins are proteins in this cell membrane that allow substances to pass through the outer membrane of Gram-negative bacteria. In Gram-positive bacteria, lipoteichoic acid anchors the cell wall to the cell membrane. Figure 3. Archaean cell walls do not have peptidoglycan. There are four different types of archaean cell walls.

One type is composed of pseudopeptidoglycan , which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein. Other differences between Bacteria and Archaea are seen in Table 4. Note that features related to DNA replication, transcription and translation in Archaea are similar to those seen in eukaryotes.

Thus, photoautotrophs use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain energy and carbon from an organic chemical source. Chemoautotrophs obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide. Finally, photoheterotrophs use light as an energy source, but require an organic carbon source they cannot fix carbon dioxide into organic carbon.

In contrast to the great metabolic diversity of prokaryotes, eukaryotes are only photoautotrophs plants and some protists or chemoheterotrophs animals, fungi, and some protists. The table below summarizes carbon and energy sources in prokaryotes. The videos below provide more detailed overviews of Archaea and Bacteria, including general features and metabolic diversity:.

In fact, Archaea and Eukarya form a monophyletic group, not Archaea and Bacteria. These relationships indicate that archaea are more closely related to eukaryotes than to bacteria, even though superficially archaea appear to be much more similar to bacteria than eukaryotes. Early life on Earth: The Earth is approximately 4.

While it is formally possible that life arose during the Hadean eon, conditions may not have been stable enough on the planet to sustain life because l arge numbers of asteroids were thought to have collided with the planet during the end of the Hadean and beginning of the Archean eons. The earliest chemical evidence of life, in the form of chemical signatures produced only by living organisms, dates to approximately 3.

What were these early life forms like? Thus the first living things were single-celled, prokaryotic anaerobes living without oxygen and likely chemotrophic. The Oxygen Revolution: The evolution of water-splitting and oxygen-generating photosynthesis by cyanobacteria led to the first free molecular oxygen about 2. The free oxygen produced by cyanobacteria immediately reacted with soluble iron in the oceans, causing iron oxide rust to precipitate out of the oceans.

Today we see evidence of the slow accumulation of oxygen in the atmosphere through banded iron formations present in sedimentary rocks from that period. The increase in oxygen is a dramatic example of how life can alter the planet. The video below provides an overview of the Oxygen Revolution aka, the Oxygen Catastrophe , including its detrimental effects on the organisms that lived at the time:.