Three-domain system

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A phylogenetic tree based on rRNA data, emphasizing the separation of bacteria, archaea, and eukaryotes, as proposed by Carl Woese, George E. Fox et al. in 1990 Phylogenetic tree of life 1990 LUCA.svg
A phylogenetic tree based on rRNA data, emphasizing the separation of bacteria, archaea, and eukaryotes, as proposed by Carl Woese, George E. Fox et al. in 1990

The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 [2] [1] that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of archaea from bacteria as completely different organism. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as eukaryotes are considered as one group of archaea. [3] [4] [5]

Contents

Background

Woese argued, on the basis of differences in 16S rRNA genes, that bacteria, archaea, and eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Originally his split of the prokaryotes was into Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990. [1]

Acceptance of the validity of Woese's phylogenetically valid classification was a slow process. Prominent biologists including Salvador Luria and Ernst Mayr objected to his division of the prokaryotes. [6] [7] Not all criticism of him was restricted to the scientific level. A decade of labor-intensive oligonucleotide cataloging left him with a reputation as "a crank," and Woese would go on to be dubbed "Microbiology's Scarred Revolutionary" by a news article printed in the journal Science in 1997. [8] The growing amount of supporting data led the scientific community to accept the Archaea by the mid-1980s. [9] Today, very few scientists still accept the concept of a unified Prokarya. [10]

Classification

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The three-domain system includes the Archaea (represented by Sulfolobus , left), Bacteria (represented by S. aureus , middle) and Eukaryote (represented by the Australian green tree frog, right)

The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the previously used five- or six-kingdom systems. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to eukaryotes than they are to other prokaryotes – bacteria-like organisms with no cell nucleus. The three-domain system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya. [3]

Domain Archaea

The Archaea are prokaryotic, with no nuclear membrane, but with biochemistry and RNA markers that are distinct from bacteria. The Archaeans possess unique, ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth, most notably their diverse, exotic metabolisms.

Some examples of archaeal organisms are:

Domain Bacteria

The Bacteria are also prokaryotic; their domain consists of cells with bacterial rRNA, no nuclear membrane, and whose membranes possess primarily diacyl glycerol diester lipids. Traditionally classified as bacteria, many thrive in the same environments favored by humans, and were the first prokaryotes discovered; they were briefly called the Eubacteria or "true" bacteria when the Archaea were first recognized as a distinct clade.

Most known pathogenic prokaryotic organisms belong to bacteria (see [11] for exceptions). For that reason, and because the Archaea are typically difficult to grow in laboratories, Bacteria are currently studied more extensively than Archaea.

Some examples of bacteria include:

Domain Eukaryota

Eukaryota are organisms whose cells contain a membrane-bound nucleus. They include many large single-celled organisms and all known non-microscopic organisms. A partial list of eukaryotic organisms includes:

Kingdom Fungi or fungi
Kingdom Plantae or plants
Kingdom Animalia or animals
Kingdom Protista or protozoans

Niches

Each of the three cell types tends to fit into recurring specialities or roles. Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans. In fact, the structure of a eukaryote is likely to have derived from a joining of different cell types, forming organelles.

Parakaryon myojinensis ( incertae sedis ) is a single-celled organism known to be a unique example. "This organism appears to be a life form distinct from prokaryotes and eukaryotes", [12] with features of both.

Alternatives

Alternative versions of the three domains of life's phylogeny 3 domains.png
Alternative versions of the three domains of life's phylogeny

Parts of the three-domain theory have been challenged by scientists including Ernst Mayr, Thomas Cavalier-Smith, and Radhey S. Gupta. [13] [14] [15]

Recent work has proposed that Eukaryota may have actually branched off from the domain Archaea. According to Spang et al. Lokiarchaeota forms a monophyletic group with eukaryotes in phylogenomic analyses. The associated genomes also encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. [16] This work suggests a two-domain system as opposed to the three-domain system. [4] [5] [3] Exactly how and when archaea, bacteria, and eucarya developed and how they are related continues to be debated. [17] [3] [18]

See also

Related Research Articles

<span class="mw-page-title-main">Carl Woese</span> American microbiologist who identified Archaea (1928–2012)

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois at Urbana–Champaign.

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

In biological taxonomy, a domain, also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.

Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, and cutis. Individuals are very small, typically only 0.2–0.3 μm in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes is Mycoplasma. Colonies show the typical "fried-egg" appearance.

<span class="mw-page-title-main">Two-empire system</span> Biological classification system

The two-empire system was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

<span class="mw-page-title-main">Neomura</span>

Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan cell walls with other glycoproteins. As of August 2017, the neomuran hypothesis is not accepted by most workers; molecular phylogenies suggest that eukaryotes are most closely related to one group of archaeans and evolved from them, rather than forming a clade with all archaeans, and that Archaea and Bacteria are sister groups.

<span class="mw-page-title-main">Monera</span> Biological kingdom that contains unicellular organisms with a prokaryotic cell organization

Monera (/məˈnɪərə/) is a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a nucleus.

<span class="mw-page-title-main">Prokaryote</span> Unicellular organism that lacks a membrane-bound nucleus

A prokaryote is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Greek πρό and κάρυον. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota. In the study of the origins of life, prokaryotes are thought to have arisen before eukaryotes.

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

<span class="mw-page-title-main">Horizontal gene transfer in evolution</span> Evolutionary consequences of transfer of genetic material between organisms of different taxa

Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer (HGT), scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.

<span class="mw-page-title-main">Eukaryote</span> Domain of life having cells with nuclei

Eukaryotes are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacteria and Archaea make up the other two domains.

<span class="mw-page-title-main">Evolution of cells</span> Evolutionary origin and subsequent development of cells

Evolution of cells refers to the evolutionary origin and subsequent evolutionary development of cells. Cells first emerged at least 3.8 billion years ago approximately 750 million years after Earth was formed.

Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.

<span class="mw-page-title-main">Eocyte hypothesis</span> Hypothesis in evolutionary biology

The eocyte hypothesis in evolutionary biology proposes the origin of eukaryotes from a group of prokaryotes called eocytes. After his team at the University of California, Los Angeles discovered eocytes in 1984, James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: Parkaryoates that include Bacteria and Archaea, and karyotes that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria.

The Woeseian revolution was the progression of the phylogenetic tree of life concept from two main divisions, known as the Prokarya and Eukarya, into three domains now classified as Bacteria, Archaea, and Eukaryotes. The discovery of the new domain stemmed from the work of biophysicist Carl Woese in 1977 from a principle of evolutionary biology designated as Woese's dogma. It states that the evolution of ribosomal RNA (rRNA) was a necessary precursor to the evolution of modern life forms. Although the three-domain system has been widely accepted, the initial introduction of Woese’s discovery received criticism from the scientific community.

<span class="mw-page-title-main">Lokiarchaeota</span> Phylum of archaea

Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group (DSAG), also known as Marine Benthic Group B (MBG-B). Lokiarchaeota is part of the superphylum Asgard containing the phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota, and Helarchaeota. A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

The biological classification system of life introduced by British zoologist Thomas Cavalier-Smith involves systematic arrangements of all life forms on earth. Following and improving the classification systems introduced by Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. His classification has been a major foundation in modern taxonomy, particularly with revisions and reorganisations of kingdoms and phyla.

<span class="mw-page-title-main">Darwinian threshold</span> Period during the evolution of the first cells

Darwinian threshold or Darwinian transition is a term introduced by Carl Woese to describe a transition period during the evolution of the first cells when genetic transmission moves from a predominantly horizontal mode to a vertical mode. The process starts when the ancestors of the Last Universal Common Ancestor become refractory to horizontal gene transfer (HGT) and become individual entities with vertical heredity upon which natural selection is effective. After this transition, life is characterized by genealogies that have a modern tree-like phylogeny.

<span class="mw-page-title-main">Marine prokaryotes</span> Marine bacteria and marine archaea

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

<span class="mw-page-title-main">Two-domain system</span> Biological classification system

The two-domain system is a biological classification by which all organisms in the tree of life are classified into two big domains, Bacteria and Archaea. It emerged from development in the knowledge of archaea diversity and challenge over the widely accepted three-domain system that defines life into Bacteria, Archaea, and Eukarya. It was predicted by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system due to better compelling evidences at the time. Better understanding of archaea, especially in their roles in the origin of eukaryotes by symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became widely appreciated after the discovery of a large group (superphylum) of archaea called Asgard in 2017, evidences of which suggest to be the evolutionary root of eukaryotes – implying that eukaryotes are members of the domain Archaea.

References

  1. 1 2 3 Woese CR, Kandler O, Wheelis ML (June 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. Bibcode:1990PNAS...87.4576W. doi: 10.1073/pnas.87.12.4576 . PMC   54159 . PMID   2112744.
  2. Woese CR, Fox GE (November 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. Bibcode:1977PNAS...74.5088W. doi: 10.1073/pnas.74.11.5088 . PMC   432104 . PMID   270744.
  3. 1 2 3 4 Gabaldón, Toni (8 October 2021). "Origin and Early Evolution of the Eukaryotic Cell". Annual Review of Microbiology. 75 (1): 631–647. doi:10.1146/annurev-micro-090817-062213. ISSN   0066-4227 . Retrieved 11 August 2022. A rooted version of this three-domain tree placed Archaea and Eukarya as sister clades, suggesting that eukaryotes were very distantly related to archaea and not more related to any specific group. More recently, phylogenetic analyses using more sophisticated models and expanded gene data sets have provided increasing support for an alternative tree topology in which the eukaryotic clade branches within Archaea, rather than next to it.
  4. 1 2 Nobs, Stephanie-Jane; MacLeod, Fraser I.; Wong, Hon Lun; Burns, Brendan P. (2022). "Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?". Trends in Microbiology. 30 (5): 421–431. doi:10.1016/j.tim.2021.11.003.
  5. 1 2 Doolittle, W. Ford (2020). "Evolution: Two Domains of Life or Three?". Current Biology. 30 (4): R177–R179. doi: 10.1016/j.cub.2020.01.010 . PMID   32097647.
  6. Mayr, Ernst (1998). "Two empires or three?". Proceedings of the National Academy of Sciences. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi: 10.1073/pnas.95.17.9720 . PMC   33883 . PMID   9707542.
  7. Sapp, Jan A. (December 2007). "The structure of microbial evolutionary theory". Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. 38 (4): 780–95. doi:10.1016/j.shpsc.2007.09.011. PMID   18053933.
  8. Morell, V. (1997-05-02). "Microbiology's scarred revolutionary". Science. 276 (5313): 699–702. doi:10.1126/science.276.5313.699. ISSN   0036-8075. PMID   9157549. S2CID   84866217.
  9. Sapp, Jan A. (2009). The new foundations of evolution: on the tree of life. New York: Oxford University Press. ISBN   978-0-199-73438-2.
  10. Koonin, Eugene (2014). "Carl Woese's vision of cellular evolution and the domains of life". RNA Biology. RNA Biol. 11 (3): 197–204. doi:10.4161/rna.27673. PMC   4008548 . PMID   24572480.
  11. Eckburg, Paul B.; Lepp, Paul W.; Relman, David A. (2003). "Archaea and their potential role in human disease". Infection and Immunity. 71 (2): 591–596. doi:10.1128/IAI.71.2.591-596.2003. PMC   145348 . PMID   12540534.
  12. Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K (2012). "Prokaryote or eukaryote? A unique microorganism from the deep sea". Journal of Electron Microscopy. 61 (6): 423–31. doi:10.1093/jmicro/dfs062. PMID   23024290.
  13. Gupta, Radhey S. (1998). "Life's Third Domain (Archaea): An Established Fact or an Endangered Paradigm?: A New Proposal for Classification of Organisms Based on Protein Sequences and Cell Structure". Theoretical Population Biology. 54 (2): 91–104. doi:10.1006/tpbi.1998.1376. PMID   9733652.
  14. Mayr, E. (1998). "Two empires or three?". Proc. Natl. Acad. Sci. USA. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi: 10.1073/pnas.95.17.9720 . PMC   33883 . PMID   9707542.
  15. Cavalier-Smith, Thomas (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". Int J Syst Evol Microbiol. 52 (1): 7–76. doi: 10.1099/00207713-52-1-7 . PMID   11837318.
  16. Spang, Anja (2015). "Complex archaea that bridge the gap between prokaryotes and eukaryotes". Nature. 521 (7551): 173–179. Bibcode:2015Natur.521..173S. doi:10.1038/nature14447. PMC   4444528 . PMID   25945739.
  17. Callier, Viviane (8 June 2022). "Mitochondria and the origin of eukaryotes". Knowable Magazine. doi: 10.1146/knowable-060822-2 . Retrieved 18 August 2022.
  18. McCutcheon, John P. (6 October 2021). "The Genomics and Cell Biology of Host-Beneficial Intracellular Infections". Annual Review of Cell and Developmental Biology. 37 (1): 115–142. doi:10.1146/annurev-cellbio-120219-024122. ISSN   1081-0706 . Retrieved 19 August 2022.