Eukaryote

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"Eukaryotic cell" redirects here. Eukaryote_sentence_0

For the journal, see Eukaryotic Cell (journal). Eukaryote_sentence_1

Eukaryote_table_infobox_0

Eukaryote

Temporal range: OrosirianPresent 1850–0 Ma


Pha.


Proterozoic



Archean

Had'nEukaryote_header_cell_0_0_0

Scientific classification EukaryotaEukaryote_header_cell_0_1_0
Domain:Eukaryote_cell_0_2_0 Eukaryota

(Chatton, 1925) Whittaker & Margulis, 1978Eukaryote_cell_0_2_1

Supergroups and kingdomsEukaryote_header_cell_0_3_0

Eukaryotes (/juːˈkærioʊts, -əts/) are organisms whose cells have a nucleus enclosed within a nuclear envelope. Eukaryote_sentence_2

Eukaryotes belong to the domain Eukaryota or Eukarya; their name comes from the Greek (eu, "well" or "good") and (karyon, "nut" or "kernel"). Eukaryote_sentence_3

The domain Eukaryota makes up one of the domains of life in the now obsolete three-domain system: The two other domains are Bacteria and Archaea (together known as prokaryotes), and the Eukaryote are usually now regarded as having emerged in the Archaea in or as sister of the now cultivated Asgard Archaea. Eukaryote_sentence_4

Eukaryotes represent a tiny minority of the number of living organisms; however, due to their generally much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryote_sentence_5

Eukaryotes emerged approximately 2.1-1.6 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs. Eukaryote_sentence_6

Eukaryotic cells typically contain membrane-bound organelles such as mitochondria and Golgi apparatus, and chloroplasts can be found in plants and algae; these organelles are unique to eukaryotes, although primitive organelles can be found in prokaryotes. Eukaryote_sentence_7

As well as being unicellular, eukaryotes may also be multicellular and include many cell types forming different kinds of tissue; in comparison, prokaryotes are typically unicellular. Eukaryote_sentence_8

Animals, plants, and fungi are the most familiar eukaryotes; other eukaryotes are sometimes called protists. Eukaryote_sentence_9

Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. Eukaryote_sentence_10

In mitosis, one cell divides to produce two genetically identical cells. Eukaryote_sentence_11

In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells. Eukaryote_sentence_12

These act as sex cells (gametes). Eukaryote_sentence_13

Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis. Eukaryote_sentence_14

History of the concept Eukaryote_section_0

The concept of the eukaryote has been attributed to the French biologist Edouard Chatton (1883–1947). Eukaryote_sentence_15

The terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. Eukaryote_sentence_16 B. van Niel in 1962. Eukaryote_sentence_17

In his 1937 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. Eukaryote_sentence_18

However he mentioned this in only one paragraph, and the idea was effectively ignored until Chatton's statement was rediscovered by Stanier and van Niel. Eukaryote_sentence_19

In 1905 and 1910, the Russian biologist Konstantin Mereschkowski (1855–1921) argued that plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic (heterotrophic) host that was itself formed by symbiosis between an amoeba-like host and a bacterium-like cell that formed the nucleus. Eukaryote_sentence_20

Plants had thus inherited photosynthesis from cyanobacteria. Eukaryote_sentence_21

In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in eukaryotic cells in her paper, On the origin of mitosing cells. Eukaryote_sentence_22

In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA. Eukaryote_sentence_23

This helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts. Eukaryote_sentence_24

In 1977, Woese and George Fox introduced a "third form of life", which they called the Archaebacteria; in 1990, Woese, Otto Kandler and Mark L. Wheelis renamed this the Archaea. Eukaryote_sentence_25

In 1979, G. W. Gould and G. J. Dring suggested that the eukaryotic cell's nucleus came from the ability of Gram-positive bacteria to form endospores. Eukaryote_sentence_26

In 1987 and later papers, Thomas Cavalier-Smith proposed instead that the membranes of the nucleus and endoplasmic reticulum first formed by infolding a prokaryote's plasma membrane. Eukaryote_sentence_27

In the 1990s, several other biologists proposed endosymbiotic origins for the nucleus, effectively reviving Mereschkowski's theory. Eukaryote_sentence_28

Cell features Eukaryote_section_1

Eukaryotic cells are typically much larger than those of prokaryotes, having a volume of around 10,000 times greater than the prokaryotic cell. Eukaryote_sentence_29

They have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments, which play an important role in defining the cell's organization and shape. Eukaryote_sentence_30

Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division. Eukaryote_sentence_31

Internal membrane Eukaryote_section_2

Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Eukaryote_sentence_32

Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Eukaryote_sentence_33

Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. Eukaryote_sentence_34

It is probable that most other membrane-bound organelles are ultimately derived from such vesicles. Eukaryote_sentence_35

Alternatively some products produced by the cell can leave in a vesicle through exocytosis. Eukaryote_sentence_36

The nucleus is surrounded by a double membrane (commonly referred to as a nuclear membrane or nuclear envelope), with pores that allow material to move in and out. Eukaryote_sentence_37

Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. Eukaryote_sentence_38

It includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Eukaryote_sentence_39

Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum. Eukaryote_sentence_40

In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus. Eukaryote_sentence_41

Vesicles may be specialized for various purposes. Eukaryote_sentence_42

For instance, lysosomes contain digestive enzymes that break down most biomolecules in the cytoplasm. Eukaryote_sentence_43

Peroxisomes are used to break down peroxide, which is otherwise toxic. Eukaryote_sentence_44

Many protozoans have contractile vacuoles, which collect and expel excess water, and extrusomes, which expel material used to deflect predators or capture prey. Eukaryote_sentence_45

In higher plants, most of a cell's volume is taken up by a central vacuole, which mostly contains water and primarily maintains its osmotic pressure. Eukaryote_sentence_46

Mitochondria and plastids Eukaryote_section_3

Mitochondria are organelles found in all but one eukaryote. Eukaryote_sentence_47

Mitochondria provide energy to the eukaryote cell by converting sugars into ATP. Eukaryote_sentence_48

They have two surrounding membranes, each a phospholipid bi-layer; the inner of which is folded into invaginations called cristae where aerobic respiration takes place. Eukaryote_sentence_49

The outer mitochondrial membrane is freely permeable and allows almost anything to enter into the intermembrane space while the inner mitochondrial membrane is semi permeable so allows only some required things into the mitochondrial matrix. Eukaryote_sentence_50

Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA. Eukaryote_sentence_51

They are now generally held to have developed from endosymbiotic prokaryotes, probably proteobacteria. Eukaryote_sentence_52

Some eukaryotes, such as the metamonads such as Giardia and Trichomonas, and the amoebozoan Pelomyxa, appear to lack mitochondria, but all have been found to contain mitochondrion-derived organelles, such as hydrogenosomes and mitosomes, and thus have lost their mitochondria secondarily. Eukaryote_sentence_53

They obtain energy by enzymatic action on nutrients absorbed from the environment. Eukaryote_sentence_54

The metamonad Monocercomonoides has also acquired, by lateral gene transfer, a cytosolic sulfur mobilisation system which provides the clusters of iron and sulfur required for protein synthesis. Eukaryote_sentence_55

The normal mitochondrial iron-sulfur cluster pathway has been lost secondarily. Eukaryote_sentence_56

Plants and various groups of algae also have plastids. Eukaryote_sentence_57

Plastids also have their own DNA and are developed from endosymbionts, in this case cyanobacteria. Eukaryote_sentence_58

They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Eukaryote_sentence_59

Others are involved in storing food. Eukaryote_sentence_60

Although plastids probably had a single origin, not all plastid-containing groups are closely related. Eukaryote_sentence_61

Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion. Eukaryote_sentence_62

The capture and sequestering of photosynthetic cells and chloroplasts occurs in many types of modern eukaryotic organisms and is known as kleptoplasty. Eukaryote_sentence_63

Endosymbiotic origins have also been proposed for the nucleus, and for eukaryotic flagella. Eukaryote_sentence_64

Cytoskeletal structures Eukaryote_section_4

Main article: Cytoskeleton Eukaryote_sentence_65

Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar structures called cilia. Eukaryote_sentence_66

Flagella and cilia are sometimes referred to as undulipodia, and are variously involved in movement, feeding, and sensation. Eukaryote_sentence_67

They are composed mainly of tubulin. Eukaryote_sentence_68

These are entirely distinct from prokaryotic flagellae. Eukaryote_sentence_69

They are supported by a bundle of microtubules arising from a centriole, characteristically arranged as nine doublets surrounding two singlets. Eukaryote_sentence_70

Flagella also may have hairs, or mastigonemes, and scales connecting membranes and internal rods. Eukaryote_sentence_71

Their interior is continuous with the cell's cytoplasm. Eukaryote_sentence_72

Microfilamental structures composed of actin and actin binding proteins, e.g., α-actinin, fimbrin, filamin are present in submembranous cortical layers and bundles, as well. Eukaryote_sentence_73

Motor proteins of microtubules, e.g., dynein or kinesin and actin, e.g., myosins provide dynamic character of the network. Eukaryote_sentence_74

Centrioles are often present even in cells and groups that do not have flagella, but conifers and flowering plants have neither. Eukaryote_sentence_75

They generally occur in groups that give rise to various microtubular roots. Eukaryote_sentence_76

These form a primary component of the cytoskeletal structure, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Eukaryote_sentence_77

Centrioles produce the spindle during nuclear division. Eukaryote_sentence_78

The significance of cytoskeletal structures is underlined in the determination of shape of the cells, as well as their being essential components of migratory responses like chemotaxis and chemokinesis. Eukaryote_sentence_79

Some protists have various other microtubule-supported organelles. Eukaryote_sentence_80

These include the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the haptophytes, which have a peculiar flagellum-like organelle called the haptonema. Eukaryote_sentence_81

Cell wall Eukaryote_section_5

Main article: Cell wall Eukaryote_sentence_82

The cells of plants and algae, fungi and most chromalveolates have a cell wall, a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. Eukaryote_sentence_83

The cell wall also prevents over-expansion when water enters the cell. Eukaryote_sentence_84

The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. Eukaryote_sentence_85

The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. Eukaryote_sentence_86

The most common hemicellulose in the primary cell wall is xyloglucan. Eukaryote_sentence_87

Differences among eukaryotic cells Eukaryote_section_6

There are many different types of eukaryotic cells, though animals and plants are the most familiar eukaryotes, and thus provide an excellent starting point for understanding eukaryotic structure. Eukaryote_sentence_88

Fungi and many protists have some substantial differences, however. Eukaryote_sentence_89

Animal cell Eukaryote_section_7

All animals are eukaryotic. Eukaryote_sentence_90

Animal cells are distinct from those of other eukaryotes, most notably plants, as they lack cell walls and chloroplasts and have smaller vacuoles. Eukaryote_sentence_91

Due to the lack of a cell wall, animal cells can transform into a variety of shapes. Eukaryote_sentence_92

A phagocytic cell can even engulf other structures. Eukaryote_sentence_93

Plant cell Eukaryote_section_8

Main article: Plant cell Eukaryote_sentence_94

Plant cells are quite different from the cells of the other eukaryotic organisms. Eukaryote_sentence_95

Their distinctive features are: Eukaryote_sentence_96

Eukaryote_unordered_list_0

Fungal cell Eukaryote_section_9

The cells of fungi are most similar to animal cells, with the following exceptions: Eukaryote_sentence_97

Eukaryote_unordered_list_1

  • A cell wall that contains chitinEukaryote_item_1_6
  • Less compartmentation between cells; the hyphae of higher fungi have porous partitions called septa, which allow the passage of cytoplasm, organelles, and, sometimes, nuclei; so each organism is essentially a giant multinucleate supercell – these fungi are described as coenocytic. Primitive fungi have few or no septa.Eukaryote_item_1_7
  • Only the most primitive fungi, chytrids, have flagella.Eukaryote_item_1_8

Other eukaryotic cells Eukaryote_section_10

Some groups of eukaryotes have unique organelles, such as the cyanelles (unusual chloroplasts) of the glaucophytes, the haptonema of the haptophytes, or the ejectosomes of the cryptomonads. Eukaryote_sentence_98

Other structures, such as pseudopodia, are found in various eukaryote groups in different forms, such as the lobose amoebozoans or the reticulose foraminiferans. Eukaryote_sentence_99

Reproduction Eukaryote_section_11

Cell division generally takes place asexually by mitosis, a process that allows each daughter nucleus to receive one copy of each chromosome. Eukaryote_sentence_100

Most eukaryotes also have a life cycle that involves sexual reproduction, alternating between a haploid phase, where only one copy of each chromosome is present in each cell and a diploid phase, wherein two copies of each chromosome are present in each cell. Eukaryote_sentence_101

The diploid phase is formed by fusion of two haploid gametes to form a zygote, which may divide by mitosis or undergo chromosome reduction by meiosis. Eukaryote_sentence_102

There is considerable variation in this pattern. Eukaryote_sentence_103

Animals have no multicellular haploid phase, but each plant generation can consist of haploid and diploid multicellular phases. Eukaryote_sentence_104

Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times. Eukaryote_sentence_105

The evolution of sexual reproduction may be a primordial and fundamental characteristic of eukaryotes. Eukaryote_sentence_106

Based on a phylogenetic analysis, Dacks and Roger proposed that facultative sex was present in the common ancestor of all eukaryotes. Eukaryote_sentence_107

A core set of genes that function in meiosis is present in both Trichomonas vaginalis and Giardia intestinalis, two organisms previously thought to be asexual. Eukaryote_sentence_108

Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, it was inferred that core meiotic genes, and hence sex, were likely present in a common ancestor of all eukaryotes. Eukaryote_sentence_109

Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus Leishmania, have been shown to have a sexual cycle. Eukaryote_sentence_110

Also, evidence now indicates that amoebae, previously regarded as asexual, are anciently sexual and that the majority of present-day asexual groups likely arose recently and independently. Eukaryote_sentence_111

Classification Eukaryote_section_12

Further information: Eukaryote_sentence_112

In antiquity, the two lineages of animals and plants were recognized. Eukaryote_sentence_113

They were given the taxonomic rank of Kingdom by Linnaeus. Eukaryote_sentence_114

Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980s. Eukaryote_sentence_115

The various single-cell eukaryotes were originally placed with plants or animals when they became known. Eukaryote_sentence_116

In 1818, the German biologist Georg A. Goldfuss coined the word protozoa to refer to organisms such as ciliates, and this group was expanded until it encompassed all single-celled eukaryotes, and given their own kingdom, the Protista, by Ernst Haeckel in 1866. Eukaryote_sentence_117

The eukaryotes thus came to be composed of four kingdoms: Eukaryote_sentence_118

Eukaryote_unordered_list_2

  • Kingdom ProtistaEukaryote_item_2_9
  • Kingdom PlantaeEukaryote_item_2_10
  • Kingdom FungiEukaryote_item_2_11
  • Kingdom AnimaliaEukaryote_item_2_12

The protists were understood to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature. Eukaryote_sentence_119

The disentanglement of the deep splits in the tree of life only really started with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain. Eukaryote_sentence_120

At the same time, work on the protist tree intensified, and is still actively going on today. Eukaryote_sentence_121

Several alternative classifications have been forwarded, though there is no consensus in the field. Eukaryote_sentence_122

Eukaryotes are a clade usually assessed to be sister to Heimdallarchaeota in the Asgard grouping in the Archaea. Eukaryote_sentence_123

In one proposed system, the basal groupings are the Opimoda, Diphoda, the Discoba, and the Loukozoa. Eukaryote_sentence_124

The Eukaryote root is usually assessed to be near or even in Discoba. Eukaryote_sentence_125

A classification produced in 2005 for the International Society of Protistologists, which reflected the consensus of the time, divided the eukaryotes into six supposedly monophyletic 'supergroups'. Eukaryote_sentence_126

However, in the same year (2005), doubts were expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata, and a review in 2006 noted the lack of evidence for several of the supposed six supergroups. Eukaryote_sentence_127

A revised classification in 2012 recognizes five supergroups. Eukaryote_sentence_128

Eukaryote_table_general_1

Archaeplastida (or Primoplantae)Eukaryote_cell_1_0_0 Land plants, green algae, red algae, and glaucophytesEukaryote_cell_1_0_1
SAR supergroupEukaryote_cell_1_1_0 Stramenopiles (brown algae, diatoms, etc.), Alveolata, and Rhizaria (Foraminifera, Radiolaria, and various other amoeboid protozoa)Eukaryote_cell_1_1_1
ExcavataEukaryote_cell_1_2_0 Various flagellate protozoaEukaryote_cell_1_2_1
AmoebozoaEukaryote_cell_1_3_0 Most lobose amoeboids and slime moldsEukaryote_cell_1_3_1
OpisthokontaEukaryote_cell_1_4_0 Animals, fungi, choanoflagellates, etc.Eukaryote_cell_1_4_1

There are also smaller groups of eukaryotes whose position is uncertain or seems to fall outside the major groups – in particular, Haptophyta, Cryptophyta, Centrohelida, Telonemia, Picozoa, Apusomonadida, Ancyromonadida, Breviatea, and the genus Collodictyon. Eukaryote_sentence_129

Overall, it seems that, although progress has been made, there are still very significant uncertainties in the evolutionary history and classification of eukaryotes. Eukaryote_sentence_130

As Roger & Simpson said in 2009 "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution." Eukaryote_sentence_131

In an article published in Nature Microbiology in April 2016 the authors, "reinforced once again that the life we see around us – plants, animals, humans and other so-called eukaryotes – represent a tiny percentage of the world's biodiversity." Eukaryote_sentence_132

They classified eukaryote "based on the inheritance of their information systems as opposed to lipid or other cellular structures." Eukaryote_sentence_133

Jillian F. Banfield of the University of California, Berkeley and fellow scientists used a super computer to generate a diagram of a new tree of life based on DNA from 3000 species including 2,072 known species and 1,011 newly reported microbial organisms, whose DNA they had gathered from diverse environments. Eukaryote_sentence_134

As the capacity to sequence DNA became easier, Banfield and team were able to do metagenomic sequencing – "sequencing whole communities of organisms at once and picking out the individual groups based on their genes alone." Eukaryote_sentence_135

Phylogeny Eukaryote_section_13

The rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved "crown" group (not technically a true crown), which was usually divided by the form of the mitochondrial cristae; see crown eukaryotes. Eukaryote_sentence_136

The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive; but this is now considered an artifact of long-branch attraction, and they are known to have lost them secondarily. Eukaryote_sentence_137

As of 2011, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizaria is not one of the main eukaryote groups; also that the Amoebozoa and Opisthokonta are each monophyletic and form a clade, often called the unikonts. Eukaryote_sentence_138

Beyond this, there does not appear to be a consensus. Eukaryote_sentence_139

It has been estimated that there may be 75 distinct lineages of eukaryotes. Eukaryote_sentence_140

Most of these lineages are protists. Eukaryote_sentence_141

The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000–220,050 Mb in the dinoflagellate Prorocentrum micans, showing that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. Eukaryote_sentence_142

The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. Eukaryote_sentence_143

Later endosymbiosis led to the spread of plastids in some lineages. Eukaryote_sentence_144

Five supergroups Eukaryote_section_14

A global tree of eukaryotes from a consensus of phylogenetic evidence (in particular, phylogenomics), rare genomic signatures, and morphological characteristics is presented in Adl et al. Eukaryote_sentence_145

2012 and Burki 2014/2016 with the picozoa having emerged within the Archaeplastida, and Cryptista as it's sister. Eukaryote_sentence_146

Possibly, TSAR is sister to the Haptista. Eukaryote_sentence_147

In some analyses, the Hacrobia group (Haptophyta + Cryptophyta) is placed next to Archaeplastida, but in other ones it is nested inside the Archaeplastida. Eukaryote_sentence_148

However, several recent studies have concluded that Haptophyta and Cryptophyta do not form a monophyletic group. Eukaryote_sentence_149

The former could be a sister group to the SAR group, the latter cluster with the Archaeplastida (plants in the broad sense). Eukaryote_sentence_150

The division of the eukaryotes into two primary clades, bikonts (Archaeplastida + SAR + Excavata) and unikonts (Amoebozoa + Opisthokonta), derived from an ancestral biflagellar organism and an ancestral uniflagellar organism, respectively, had been suggested earlier. Eukaryote_sentence_151

A 2012 study produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense. Eukaryote_sentence_152

A highly converged and congruent set of trees appears in Derelle et al. Eukaryote_sentence_153

(2015), Ren et al. Eukaryote_sentence_154

(2016), Yang et al. Eukaryote_sentence_155

(2017) and Cavalier-Smith (2015) including the supplementary information, resulting in a more conservative and consolidated tree. Eukaryote_sentence_156

It is combined with some results from Cavalier-Smith for the basal Opimoda. Eukaryote_sentence_157

The main remaining controversies are the root, and the exact positioning of the Rhodophyta and the bikonts Rhizaria, Haptista, Cryptista, Picozoa and Telonemia, many of which may be endosymbiotic eukaryote-eukaryote hybrids. Eukaryote_sentence_158

Archaeplastida acquired chloroplasts probably by endosymbiosis of a prokaryotic ancestor related to a currently extant cyanobacterium, Gloeomargarita lithophora. Eukaryote_sentence_159

Cavalier-Smith's tree Eukaryote_section_15

Thomas Cavalier-Smith 2010, 2013, 2014, 2017 and 2018 places the eukaryotic tree's root between Excavata (with ventral feeding groove supported by a microtubular root) and the grooveless Euglenozoa, and monophyletic Chromista, correlated to a single endosymbiotic event of capturing a red-algae. Eukaryote_sentence_160

He et al. Eukaryote_sentence_161

specifically supports rooting the eukaryotic tree between a monophyletic Discoba (Discicristata + Jakobida) and an Amorphea-Diaphoretickes clade. Eukaryote_sentence_162

Origin of eukaryotes Eukaryote_section_16

The origin of the eukaryotic cell is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. Eukaryote_sentence_163

A number of approaches have been used to find the first eukaryote and their closest relatives. Eukaryote_sentence_164

The last eukaryotic common ancestor (LECA) is the hypothetical last common ancestor of all eukaryotes that have ever lived, and was most likely a biological population. Eukaryote_sentence_165

Eukaryotes have a set of signature features that differentiate them from other domains of life, including an endomembrane system and unique biochemical pathways such as sterane synthesis. Eukaryote_sentence_166

A set of proteins called eukaryotic signature proteins (ESPs) was proposed to identify eukaryotic relatives in 2002: they have no homology to proteins known in other domains of life by then, but they appear to be universal among eukaryotes. Eukaryote_sentence_167

They include proteins that make up the cytoskeleton, the complex transcription machinery, membrane-sorting systems, the nuclear pore, as well as some enzymes in the biochemical pathways. Eukaryote_sentence_168

Fossils Eukaryote_section_17

The timing of this series of events is hard to determine; Knoll (2006) suggests they developed approximately 1.6–2.1 billion years ago. Eukaryote_sentence_169

Some acritarchs are known from at least 1.65 billion years ago, and the possible alga Grypania has been found as far back as 2.1 billion years ago. Eukaryote_sentence_170

The Geosiphon-like fossil fungus Diskagma has been found in paleosols 2.2 billion years old. Eukaryote_sentence_171

Organized living structures have been found in the black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryote_sentence_172

Eukaryotic life could have evolved at that time. Eukaryote_sentence_173

Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a red algae, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago. Eukaryote_sentence_174

Biomarkers suggest that at least stem eukaryotes arose even earlier. Eukaryote_sentence_175

The presence of steranes in Australian shales indicates that eukaryotes were present in these rocks dated at 2.7 billion years old, although it was suggested they could originate from samples contamination. Eukaryote_sentence_176

Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive uptick in the zinc composition of marine sediments  million years ago has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes. Eukaryote_sentence_177

In April 2019, biologists reported that the very large medusavirus, or a relative, may have been responsible, at least in part, for the evolutionary emergence of complex eukaryotic cells from simpler prokaryotic cells. Eukaryote_sentence_178

Relationship to Archaea Eukaryote_section_18

The nuclear DNA and genetic machinery of eukaryotes is more similar to Archaea than Bacteria, leading to a controversial suggestion that eukaryotes should be grouped with Archaea in the clade Neomura. Eukaryote_sentence_179

In other respects, such as membrane composition, eukaryotes are similar to Bacteria. Eukaryote_sentence_180

Three main explanations for this have been proposed: Eukaryote_sentence_181

Eukaryote_unordered_list_3

  • Eukaryotes resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a eubacterium, and the nucleus from an archaeon, from a virus, or from a pre-cell.Eukaryote_item_3_13
  • Eukaryotes developed from Archaea, and acquired their eubacterial characteristics through the endosymbiosis of a proto-mitochondrion of eubacterial origin.Eukaryote_item_3_14
  • Eukaryotes and Archaea developed separately from a modified eubacterium.Eukaryote_item_3_15

Alternative proposals include: Eukaryote_sentence_182

Eukaryote_unordered_list_4

  • The chronocyte hypothesis postulates that a primitive eukaryotic cell was formed by the endosymbiosis of both archaea and bacteria by a third type of cell, termed a chronocyte. This is mainly to account for the fact that eukaryotic signature proteins were not found anywhere else by 2002.Eukaryote_item_4_16
  • The universal common ancestor (UCA) of the current tree of life was a complex organism that survived a mass extinction event rather than an early stage in the evolution of life. Eukaryotes and in particular akaryotes (Bacteria and Archaea) evolved through reductive loss, so that similarities result from differential retention of original features.Eukaryote_item_4_17

Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea and Eukaryota in which each is monophyletic. Eukaryote_sentence_183

These are labelled 1 to 3 in the table below. Eukaryote_sentence_184

The eocyte hypothesis is a modification of hypothesis 2 in which the Archaea are paraphyletic. Eukaryote_sentence_185

(The table and the names for the hypotheses are based on Harish and Kurland, 2017.) Eukaryote_sentence_186

In recent years, most researchers have favoured either the three domains (3D) or the eocyte hypothesis. Eukaryote_sentence_187

An rRNA analyses supports the eocyte scenario, apparently with the Eukaryote root in Excavata. Eukaryote_sentence_188

A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the Asgard archaea, is: Eukaryote_sentence_189

In this scenario, the Asgard group is seen as a sister taxon of the TACK group, which comprises Crenarchaeota (formerly named eocytes), Thaumarchaeota, and others. Eukaryote_sentence_190

This group is reported contain many of the eukaryotic signature proteins and produce vesicles. Eukaryote_sentence_191

In 2017, there has been significant pushback against this scenario, arguing that the eukaryotes did not emerge within the Archaea. Eukaryote_sentence_192

Cunha et al. Eukaryote_sentence_193

produced analyses supporting the three domains (3D) or Woese hypothesis (2 in the table above) and rejecting the eocyte hypothesis (4 above). Eukaryote_sentence_194

Harish and Kurland found strong support for the earlier two empires (2D) or Mayr hypothesis (1 in the table above), based on analyses of the coding sequences of protein domains. Eukaryote_sentence_195

They rejected the eocyte hypothesis as the least likely. Eukaryote_sentence_196

A possible interpretation of their analysis is that the universal common ancestor (UCA) of the current tree of life was a complex organism that survived an evolutionary bottleneck, rather than a simpler organism arising early in the history of life. Eukaryote_sentence_197

On the other hand, the researchers who came up with Asgard re-affirmed their hypothesis with additional Asgard samples. Eukaryote_sentence_198

Details of the relation of Asgard archaea members and eukaryotes are still under consideration, although, in January 2020, scientists reported that Candidatus Prometheoarchaeum syntrophicum, a type of cultured Asgard archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago. Eukaryote_sentence_199

Endomembrane system and mitochondria Eukaryote_section_19

The origins of the endomembrane system and mitochondria are also unclear. Eukaryote_sentence_200

The phagotrophic hypothesis proposes that eukaryotic-type membranes lacking a cell wall originated first, with the development of endocytosis, whereas mitochondria were acquired by ingestion as endosymbionts. Eukaryote_sentence_201

The syntrophic hypothesis proposes that the proto-eukaryote relied on the proto-mitochondrion for food, and so ultimately grew to surround it. Eukaryote_sentence_202

Here the membranes originated after the engulfment of the mitochondrion, in part thanks to mitochondrial genes (the hydrogen hypothesis is one particular version). Eukaryote_sentence_203

In a study using genomes to construct supertrees, Pisani et al. Eukaryote_sentence_204

(2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy between an archaea closely related to Thermoplasmatales and an α-proteobacterium, likely a symbiosis driven by sulfur or hydrogen. Eukaryote_sentence_205

The mitochondrion and its genome is a remnant of the α-proteobacterial endosymbiont. Eukaryote_sentence_206

The majority of the genes from the symbiont have been transferred to the nucleus. Eukaryote_sentence_207

They make up most of the metabolic and energy-related pathways of the eukaryotic cell, while the information system is retained from archaea. Eukaryote_sentence_208

Hypotheses Eukaryote_section_20

Different hypotheses have been proposed as to how eukaryotic cells came into existence. Eukaryote_sentence_209

These hypotheses can be classified into two distinct classes – autogenous models and chimeric models. Eukaryote_sentence_210

Autogenous models Eukaryote_section_21

Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria. Eukaryote_sentence_211

According to this model, a large prokaryote developed invaginations in its plasma membrane in order to obtain enough surface area to service its cytoplasmic volume. Eukaryote_sentence_212

As the invaginations differentiated in function, some became separate compartments – giving rise to the endomembrane system, including the endoplasmic reticulum, golgi apparatus, nuclear membrane, and single membrane structures such as lysosomes. Eukaryote_sentence_213

Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium, and it is assumed that all the eukaryotic lineages that did not acquire mitochondria became extinct, a statement criticized for its lack of falsifiability. Eukaryote_sentence_214

Chloroplasts came about from another endosymbiotic event involving cyanobacteria. Eukaryote_sentence_215

Since all known eukaryotes have mitochondria, but not all have chloroplasts, the serial endosymbiosis theory proposes that mitochondria came first. Eukaryote_sentence_216

Chimeric models Eukaryote_section_22

Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. Eukaryote_sentence_217

The closest living relatives of these appears to be Asgardarchaeota and (distantly related) the alphaproteobacteria. Eukaryote_sentence_218

These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell. Eukaryote_sentence_219

Within these chimeric models, some studies further claim that mitochondria originated from a bacterial ancestor while others emphasize the role of endosymbiotic processes behind the origin of mitochondria. Eukaryote_sentence_220

The inside-out hypothesis Eukaryote_section_23

The inside-out hypothesis, developed by cousins David and Buzz Baum, suggest the fusion between free-living mitochondria-like bacteria and an archaeon into a eukaryotic cell happened gradually over a long period of time, instead of phagocytosis in a single gulp. Eukaryote_sentence_221

In this scenario, an archaeon would trap aerobic bacteria with cell protrusions, and then keep them alive to draw energy from them instead of digesting them. Eukaryote_sentence_222

During the early stages the bacteria would still be partly in direct contact with the environment, and the archaeon would not have to provide them with all the required nutrients. Eukaryote_sentence_223

But eventually the archaeon would engulf the bacteria completely, creating the internal membrane structures and nucleus membrane in the process. Eukaryote_sentence_224

It is assumed the archaean group called halophiles went through a similar procedure, where they acquired as much as a thousand genes from a bacterium, way more than through the conventional horizontal gene transfer that often occurs in the microbial world, but that the two microbes separated again before they had fused into a single eukaryote-like cell. Eukaryote_sentence_225

Based on the process of mutualistic symbiosis, the hypotheses can be categorized as – the serial endosymbiotic hypothesis or theory (SET), the hydrogen hypothesis (mostly a process of symbiosis where hydrogen transfer takes place among different species), and the syntrophy hypothesis. Eukaryote_sentence_226

These hypotheses are discussed separately in the following sections. Eukaryote_sentence_227

An expanded version of the inside-out hypothesis proposes that the eukaryotic cell was created by physical interactions between two prokaryotic organisms and that the last common ancestor of eukaryotes got its genome from a whole population or community of microbes participating in cooperative relationships to thrive and survive in their environment. Eukaryote_sentence_228

The genome from the various types of microbes would complement each other, and occasional horizontal gene transfer between them would be largely to their own benefit. Eukaryote_sentence_229

This accumulation of beneficial genes gave rise to the genome of the eukaryotic cell, which contained all the genes required for independence. Eukaryote_sentence_230

The serial endosymbiotic hypothesis Eukaryote_section_24

According to serial endosymbiotic theory (championed by Lynn Margulis), a union between a motile anaerobic bacterium (like Spirochaeta) and a thermoacidophilic crenarchaeon (like Thermoplasma which is sulfidogenic in nature) gave rise to the present day eukaryotes. Eukaryote_sentence_231

This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Eukaryote_sentence_232

Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Eukaryote_sentence_233

Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). Eukaryote_sentence_234

In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. Eukaryote_sentence_235

The bacterium on the other hand, contributed the necessary fermentation products and electron acceptors along with its motility feature to the archaeon thereby gaining a swimming motility for the organism. Eukaryote_sentence_236

From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Eukaryote_sentence_237

Spirochetes gave rise to the motile features of eukaryotic cells. Eukaryote_sentence_238

Endosymbiotic unifications of the ancestors of alpha-proteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. Eukaryote_sentence_239

For example, Thiodendron has been known to have originated via an ectosymbiotic process based on a similar syntrophy of sulfur existing between the two types of bacteria – Desulphobacter and Spirochaeta. Eukaryote_sentence_240

However, such an association based on motile symbiosis has never been observed practically. Eukaryote_sentence_241

Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments. Eukaryote_sentence_242

The hydrogen hypothesis Eukaryote_section_25

In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alpha-proteobacterium (the symbiont) gave rise to the eukaryotes. Eukaryote_sentence_243

The host utilized hydrogen (H2) and carbon dioxide (CO 2) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and CO 2 as byproducts of anaerobic fermentation process. Eukaryote_sentence_244

The host's methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation. Eukaryote_sentence_245

Endosymbiotic gene transfer (EGT) acted as a catalyst for the host to acquire the symbionts' carbohydrate metabolism and turn heterotrophic in nature. Eukaryote_sentence_246

Subsequently, the host's methane forming capability was lost. Eukaryote_sentence_247

Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. Eukaryote_sentence_248

In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes. Eukaryote_sentence_249

The syntrophy hypothesis Eukaryote_section_26

The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. Eukaryote_sentence_250

According to this theory, the origin of eukaryotic cells was based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a delta-proteobacterium. Eukaryote_sentence_251

This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. Eukaryote_sentence_252

In earlier stages, an alpha-proteobacterium became a member of this integration, and later developed into the mitochondrion. Eukaryote_sentence_253

Gene transfer from a delta-proteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. Eukaryote_sentence_254

The archaeon constituted the genetic apparatus, while the delta-proteobacterium contributed towards the cytoplasmic features. Eukaryote_sentence_255

This theory incorporates two selective forces at the time of nucleus evolution Eukaryote_sentence_256

Eukaryote_unordered_list_5

  • presence of metabolic partitioning to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, andEukaryote_item_5_18
  • prevention of abnormal protein biosynthesis due to a vast spread of introns in the archaeal genes after acquiring the mitochondrion and losing methanogenesis.Eukaryote_item_5_19
6+ serial endosymbiosis scenario Eukaryote_section_27

Pitts and Galbanón propose a complex scenario of 6+ serial endosymbiotic events of Archaea and bacteria in which mitochondria and an asgard related archaeota were acquired at a late stage of eukaryogenesis, possibly in combination, as a secondary endosymbiont. Eukaryote_sentence_257

The findings have been rebuked as an artefact. Eukaryote_sentence_258

See also Eukaryote_section_28

Eukaryote_unordered_list_6


Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Eukaryote.