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Archaea

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Archaea

Archaea (Archeabacteria)
Temporal range: Paleoarchean or perhaps Eoarchean – Recent
Halobacteria sp. strain NRC-1,
each cell about 5 μm long
Scientific classification
Domain: Archaea
Woese, Kandler & Wheelis, 1990
Kingdoms and phyla

Crenarchaeota
Euryarchaeota
Korarchaeota
Nanoarchaeota
Thaumarchaeota

The Archaea ( or ; singular archaeon) constitute a organelles in their cells.

Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Kingdom Monera), but this classification is outdated.[1] Archaeal cells have unique properties separating them from the other two domains of life: Bacteria and Eukaryota. The Archaea are further divided into four recognized phyla. Classification is difficult because the majority have not been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat and square-shaped cells of ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species forms spores.

Archaea were initially viewed as biotechnology.

Contents

  • Classification 1
    • New domain 1.1
    • Current classification 1.2
      • Species 1.2.1
  • Origin and evolution 2
    • Comparison to other domains 2.1
    • Relationship to other prokaryotes 2.2
    • Relation to eukaryotes 2.3
  • Morphology 3
  • Structure, composition development, operation 4
    • Membranes 4.1
    • Wall and flagella 4.2
  • Metabolism 5
  • Genetics 6
    • Gene transfer and genetic exchange 6.1
  • Reproduction 7
  • Ecology 8
    • Habitats 8.1
    • Role in chemical cycling 8.2
    • Interactions with other organisms 8.3
      • Mutualism 8.3.1
      • Commensalism 8.3.2
  • Significance in technology and industry 9
  • See also 10
  • References 11
  • Further reading 12
  • External links 13

Classification

New domain

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their phylogenetics, is the main method used today.

Archaea were first found in extreme environments, such as volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National Park.

Archaea were first classified as a separate group of prokaryotes in 1977 by Domains: the Eukarya, the Bacteria and the Archaea,[7] in what is now known as "The Woesian Revolution".

The word archaea comes from the cultured in the laboratory.[12][13]

Current classification

The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors.[14] These classifications rely heavily on the use of the sequence of

  • The enantiomers
  • Bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids.[82] The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. Ether bonds are chemically more resistant than ester bonds. This stability might help archaea to survive extreme temperatures and very acidic or alkaline environments.[83] Bacteria and eukaryotes do contain some ether lipids, but in contrast to archaea these lipids are not a major part of their membranes.

These phospholipids are unusual in four ways:

Archaeal membranes are made of molecules that differ strongly from those in other life forms, showing that archaea are related only distantly to bacteria and eukaryotes.[81] In all organisms cell membranes are made of molecules known as phospholipids. These molecules possess both a polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer.

Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7, D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea.

Membranes

[80] and is enclosed by an outer membrane.vesicles, which possess a particularly large periplasm that contains membrane-bound Ignicoccus; the exception to this general rule is periplasmic space. Most have a single plasma membrane and cell wall, and lack a Gram-positive bacteria Structurally, archaea are most similar to [79].flagella and they swim using one or more cell wall are usually bounded by a cell membranes Like bacteria, archaea [43] Archaea and bacteria have generally similar

Structure, composition development, operation

Some species form aggregates or filaments of cells up to 200 μm long.[67] These organisms can be prominent in biofilms.[74] Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells.[75] Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration.[76] The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors.[77] Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to 15 centimetres (5.9 in) long; these filaments are made of a particular bacteria species.[78]

[73].amoebae means that the cells have irregular shapes, and can resemble cell wall the lack of a Ferroplasma and Thermoplasma In [72] Individual archaea range from 0.1 

The sizes of prokaryotic cells relative to other cells and biomolecules (logarithmic scale)

Morphology

Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Crenarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota[61] and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer.[62] The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea,[63][64] and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure.[65] An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea.[66]

The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two.

Relation to eukaryotes

[60] and studies that suggest that Gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.[59] Gupta's proposal is also supported by other work investigating protein structural relationships[58] Cavalier-Smith has made a similar suggestion.[57][56]

The relationship between the three domains is of central importance for understanding the origin of life. Most of the metabolic pathways, which comprise the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya.[50] Within prokaryotes, archaeal cell structure is most similar to that of Gram-positive bacteria, largely because both have a single lipid bilayer[51] and usually contain a thick sacculus of varying chemical composition.[52] In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria.[51] Archaea and Gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I;[51][53] however, the phylogeny of these genes was interpreted to reveal interdomain gene transfer,[54][55] and might not reflect the organismal relationships.

Relationship to other prokaryotes

[49] One property unique to Archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in Bacteria and Eukarya, which may be a contributing factor to the ability of many Archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity. Another unique feature of Archaea is that no other known organisms are capable of methanogenesis (the metabolic production of methane). Methanogenic Archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are Bacteria, as they are often a major source of methane in such environments and can play a role as primary producers.

Woese used his new rRNA comparison method to categorize and contrast different organisms. He sequenced a variety of different species and happened upon a group of methanogens that had vastly different patterns than any known prokaryotes or eukaryotes.[46] These methanogens were much more similar to each other than they were to other organisms sequenced, leading Woese to propose the new domain of Archaea.[46] One of the interesting results of his experiments was that the Archaea were more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure.[48] This led to the conclusion that Archaea and Eukarya shared a more recent common ancestor than Eukarya and Bacteria in general.[48] The development of the nucleus occurred after the split between Bacteria and this common ancestor.[48] Although Archaea are prokaryotic, they are more closely related to Eukarya and thus cannot be placed within either the Bacteria or Eukarya domains.[7]

Archaea were split into a third domain because of the large differences in their ribosomal RNA structure. The particular RNA molecule sequenced, known as 16s rRNA, is present in all organisms and always has the same function. 16s rRNA is used for protein production. Protein production is fundamental to life and therefore any organisms with mutations of its 16s rRNA are unlikely to survive. 16s rRNA thus does not change as much as other RNA. If an organism were to mutate its rRNA, it may lack some vital proteins and die as a result. 16s rRNA is also large enough to retain organism-specific information, but small enough to be manageably sequenced in a reasonable amount of time. In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that involved splitting the RNA into fragments that could be sorted and compared to other fragments from other organisms.[46] The more similar the patterns between species were, the more closely related the organisms.[47]

Property Archaea Bacteria Eukarya
Cell Membrane Ether-linked lipids, pseudopeptidoglycan Ester-linked lipids, peptidoglycan Ester-linked lipids, various structures
Gene Structure Circular chromosomes, similar translation and transcription to Eukarya Circular chromosomes, unique translation and transcription Multiple, linear chromosomes, similar translation and transcription to Archaea
Internal Cell Structure No membrane-bound organelles or nucleus No membrane-bound organelles or nucleus Membrane-bound organelles and nucleus
Metabolism [45] Various, with methanogenesis unique to Archaea Various, including photosynthesis, aerobic and anaerobic respiration, fermentation, and autotrophy Photosynthesis and cellular respiration
Reproduction Asexual reproduction, horizontal gene transfer Asexual reproduction, horizontal gene transfer Sexual and asexual reproduction

The following table compares some major characteristics of the three domains, to illustrate their similarities and differences.[44] Many of these characteristics are also discussed below.

Comparison to other domains

[43]s only surviving meaning is "not a eukaryote", limiting its value.prokaryote' Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term [42] is that this occurred before the [41][40] One possibility[40][39] Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.

[38] The archaeal lineage may be the most ancient that exists on Earth.[37], which include Earth's oldest sediments, formed 3.8 billion years ago.Isua district. The oldest such traces come from the Greenland Such lipids have also been detected in even older rocks from west [36] such data have since been questioned.[35] dating from 2.7 billion years ago;shales Some publications suggest that archaeal or eukaryotic lipid remains are present in [34] Although probable prokaryotic cell

Scientific evidence suggests that life began on Earth at least 3.5 billion years ago.[28][29] The earliest evidences for life on Earth are graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland[30] and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia.[31][32]

Phylogenetic tree showing the relationship between the Archaea and other domains of life. Eukaryotes are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al. (2006)[1]

Origin and evolution

Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy.[15] Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, indicating that the diversity among these organisms remains obscure.[26] The Bacteria also contain many uncultured microbes with similar implications for characterization.[27]

Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[23] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability.[24] A second concern is to what extent such species designations have practical meaning.[25]

The classification of archaea into species is also controversial. Biology defines a but not with others) is of no help because archaea reproduce asexually.[22]

Species

The ARMAN are a new group of archaea recently discovered in acid mine drainage.

A superphylum - TACK - has been proposed that includes the Aigarchaeota, Crenarchaeota, Korarchaeota and Thaumarchaeota.[21] This superphylum may be related to the origin of eukaryotes.

[20]. Just as a right hand does not fit easily into a left-handed glove, a right-handed phospholipid generally cannot be used or made by enzymes adapted for the left-handed form. This suggests that archaea use entirely different enzymes for synthesizing phospholipids than do bacteria and eukaryotes. Such enzymes developed very early in life's history, suggesting an early split from the other two domains.[81]

  • Archaeal lipid tails are chemically different from other organisms. Archaeal lipids are based upon the [85]
  • In some archaea the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two independent phospholipid molecules into a single molecule with two polar heads (a [87]

Wall and flagella

Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall.[73] In most archaea the wall is assembled from surface-layer proteins, which form an S-layer.[88] An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail).[89] This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane.[90] Unlike bacteria, archaea lack peptidoglycan in their cell walls.[91] Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid.[90]

Archaea flagella operate like bacterial flagella—their long stalks are driven by rotatory motors at the base. These motors are powered by the proton gradient across the membrane. However, archaeal flagella are notably different in composition and development.[79] The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system,[92][93] while archaeal flagella appear to have evolved from bacterial type IV pili.[94] In contrast to the bacterial flagellum, which is hollow and is assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.[95]

Metabolism

Archaea exhibit a great variety of chemical reactions in their anaerobic methane oxidisers.[96] In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor. The energy released generates adenosine triphosphate (ATP) through chemiosmosis, in the same basic process that happens in the mitochondrion of eukaryotic cells.[97]

Archaea that grow in the hot water of the Morning Glory Hot Spring in Yellowstone National Park produce a bright colour

Other groups of archaea use sunlight as a source of energy (they are corals,[179] and in the region of soil that surrounds plant roots (the rhizosphere).[180][181]

Significance in technology and industry

Extant Life phyla/divisions by domain
Archaea
Eukaryote
Types
Notable
extremophiles
Archaea
Related articles
Prokaryotes: Archaea classification
Euryarchaeota
Crenarchaeota
Thaumarchaeota
Korarchaeota
Nanoarchaeota
Aigarchaeota
  • Browse any completed archaeal genome at UCSC
  • Comparative Analysis of Archaeal Genomes (at DOE's IMG system)

Genomics

  • NCBI taxonomy page on Archaea
  • Genera of the domain Archaea – list of Prokaryotic names with Standing in Nomenclature
  • Tree of Life illustration showing how Archaea relates to other lifeforms
  • Shotgun sequencing finds nanoorganisms – discovery of the ARMAN group of archaea

Classification

  • Introduction to the Archaea, ecology, systematics and morphology
  • Oceans of Archaea – E.F. DeLong, ASM News, 2003

General

External links

  • Howland, John L. (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press.  
  • Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed.). Englewood Cliffs, N.J: Prentice Hall.  
  • Garrett RA, Klenk H (2005). Archaea: Evolution, Physiology and Molecular Biology. WileyBlackwell.  
  • Cavicchioli R (2007). Archaea: Molecular and Cellular Biology. American Society for Microbiology.  
  • Blum P (editor) (2008). Archaea: New Models for Prokaryotic Biology. Caister Academic Press.  
  • Lipps G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends. Caister Academic Press.  
  • Sapp, Jan (2009). The New Foundations of Evolution. On the Tree of Life. New York: Oxford University Press.  
  • Schaechter, M (2009). Archaea (Overview) in The Desk Encyclopedia of Microbiology, 2nd edition. San Diego and London: Elsevier Academic Press.  

Further reading

  1. ^ Pace NR (May 2006). "Time for a change". Nature 441 (7091): 289.  
  2. ^ Stoeckenius W (1 October 1981). "Walsby's square bacterium: fine structure of an orthogonal procaryote". J. Bacteriol. 148 (1): 352–60.  
  3. ^ Dunn, Rob. "After 2 Years Scientists Still Can't Solve Belly Button Mystery, Continue Navel-Gazing". Guest Blog. Scientific American. Retrieved 16 January 2013. 
  4. ^ Staley JT (2006). "The bacterial species dilemma and the genomic-phylogenetic species concept". Philosophical Transactions of the Royal Society B 361 (1475): 1899–909.  
  5. ^ Zuckerkandl E, Pauling L; Pauling (1965). "Molecules as documents of evolutionary history". J. Theor. Biol. 8 (2): 357–66.  
  6. ^ Woese C, Fox G; Fox (1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–90.  
  7. ^ a b >Woese CR, Kandler O, Wheelis ML; Kandler; Wheelis (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–9.  
  8. ^ archaea. (2008). In Merriam-Webster Online Dictionary. Retrieved July 1, 2008, from http://www.merriam-webster.com/dictionary/archaea
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References

See also

Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus. These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.[188]

In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. Methanogenic archaea are a vital part of anaerobic digestion and produce biogas.[186] In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.[187]

[185]. Consequently the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.structural biology This stability makes them easier to use in [183] Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen

Commensalism

Halophiles, including the genus Cenarchaeum symbiosum, archaea reside inside the protozoa and consume hydrogen produced in their Plagiopyla frontata In anaerobic protozoa, such as

One well-understood example of mutualism is the interaction between protozoa and methanogenic archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites.[172] In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy.[173]

Mutualism

cells. Thermoplasmatales in that the ultrasmall ARMAN cells are usually seen independent of the Nanarchaeaum–Ignicoccus The nature of this relationship is unknown. However, it is distinct from that of [171] The well-characterized interactions between archaea and other organisms are either

Methanogenic archaea form a symbiosis with termites.

Interactions with other organisms

Global methane levels in 2011 had increased by a factor of 2.5 since pre-industrial times: from 722 ppb to 1800 ppb, the highest value in at least 800,000 years.[163] Methane has an anthropogenic global warming potential (AGWP) of 29, which means that it's 29 times stronger in heat-trapping than carbon dioxide is, over a 100-year time scale.[164]

Methanogens are the primary source of atmospheric methane, and are responsible for most of the world's methane emissions.[162] As a consequence, these archaea contribute to global greenhouse gas emissions and global warming.

In the decomposers in anaerobic ecosystems, such as sediments, marshes and sewage-treatment works.[161]

In the acid mine drainage and other environmental damage.[160]

[159] Archaea carry out many steps in the

Archaea recycle elements such as carbon, nitrogen and sulfur through their various habitats. Although these activities are vital for normal ecosystem function, archaea can also contribute to human-made changes, and even cause pollution.

Role in chemical cycling

[154][153] Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the [147] Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. For example, archaea are common in cold oceanic environments such as polar seas.

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life.[144] Some extremophile habitats are not dissimilar to those on Mars,[145] leading to the suggestion that viable microbes could be transferred between planets in meteorites.[146]

Other archaea exist in very acidic or alkaline conditions.[140] For example, one of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 molar sulfuric acid.[143]

[142] lives within (is an endosymbiont of) the sponge Axinella mexicana.[176]

Extremophile archaea are members of four main acidophiles.[140] These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification.

Image of plankton (light green) in the oceans; archaea form a major part of oceanic life.

Archaea exist in a broad range of habitats, and as a major part of global ecosystems,[11] may contribute up to 20% of earth's biomass.[139] The first-discovered archaeans were extremophiles.[96] Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water. However, archaea include mesophiles that grow in mild conditions, in marshland, sewage, the oceans, the intestinal tract of animals, and soils.[11]

Habitats

Ecology

Both bacteria and eukaryotes, but not archaea, make spores.[137] Some species of Haloarchaea undergo phenotypic switching and grow as several different cell types, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.[138]

Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does not occur, so if a species of archaea exists in more than one form, all have the same genetic material.[67] Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides.[135] Details have only been investigated in the genus Sulfolobus, but that cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting-points (origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes.[136] However, the proteins that direct cell division, such as the protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents.[135]

Reproduction

When the hyperthermophilic archaea Sulfolobus solfataricus[131] and Sulfolobus acidocaldarius[132] are exposed to the DNA damaging agents UV irradiation, bleomycin or mitomycin C, species-specific cellular aggregation is induced. Aggregation in S. solfataricus could not be induced by other physical stressors, such as pH or temperature shift,[131] suggesting that aggregation is induced specifically by DNA damage. Ajon et al.[132] showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in S. acidocaldarius. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al.[131][133] and Ajon et al.[132] hypothesized that cellular aggregation enhances species specific DNA transfer between Sulfolobus cells in order to provide increased repair of damaged DNA by means of homologous recombination. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.[134]

Halobacterium volcanii, an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.[130]

Gene transfer and genetic exchange

Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria, with the archaeal RNA polymerase and ribosomes being very close to their equivalents in eukaryotes.[111] Although archaea only have one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter.[125] However, other archaeal transcription factors are closer to those found in bacteria.[126] Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes,[127] and introns may occur in a few protein-encoding genes.[128][129]

Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function.[123] Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.[124]

Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops.[117] These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales.[118] Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 ("Pleolipoviridae") infecting halophilic archaea[119] and the other one by the Aeropyrum coil-shaped virus ("Spiraviridae") infecting a hyperthermophilic (optimal growth at 90–95 °C) host.[120] Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.[121][122]

Sulfolobus infected with the DNA virus STSV1.[116] Bar is 1 micrometer.

Archaea usually have a single circular chromosome,[111] the size of which may be as great as 5,751,492 base pairs in Methanosarcina acetivorans,[112] the largest known archaeal genome. One-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes.[113] Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.[114][115]

Genetics

Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase.[67] This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.[110]

Other archaea use CO
2 in the photosynthesis.[107] Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales[108][109] to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.[97]

Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models.[103]

Some Euryarchaeota are biogas.[102]

Nutritional types in archaeal metabolism
Nutritional type Source of energy Source of carbon Examples
 Phototrophs   Sunlight   Organic compounds   Halobacteria 
 Lithotrophs  Inorganic compounds  Organic compounds or carbon fixation  Ferroglobus, Methanobacteria or Pyrolobus 
 Organotrophs  Organic compounds   Organic compounds or carbon fixation   Pyrococcus, Sulfolobus or Methanosarcinales 

[99]

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