Eukaryote
Eukaryota or Eukarya, whose members are known as eukaryotes (/juːˈkærioʊts, -əts/), is a diverse domain of organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are eukaryotes. They constitute a major group of living things, along with the two groups of prokaryotes, the Bacteria and the Archaea.
Eukaryota | |
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Scientific classification ![]() | |
Domain: | Eukaryota (Chatton, 1925) Whittaker & Margulis, 1978 |
Supergroups and kingdoms | |
see text | |
The eukaryotes emerged in the Archaea or as a sister of the Asgard archaea. This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea. Eukaryotes represent a small minority of the number of organisms, but, due to their generally much larger size, their collective global biomass is about equal to that of prokaryotes. Eukaryotes emerged approximately 2.2 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs.
Eukaryotic cells contain membrane-bound organelles such as mitochondria and Golgi apparatus; plants and algae contain chloroplasts as well. Eukaryotes may be either unicellular or multicellular. In comparison, prokaryotes are typically unicellular. Other eukaryotes, mainly unicellular, are sometimes called protists. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion.
Features
Eukaryotic cells contain a nucleus.[1] This defining feature gives them their name, from the Greek εὖ (eu, "well" or "good") and κάρυον (karyon, "nut" or "kernel").[2] Eukaryotic cells are typically much larger than those of prokaryotes, having a volume of around 10,000 times greater.[3] 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. Eukaryotic DNA is divided into linear bundles called chromosomes;[4] these are separated into two matching sets by a microtubular spindle during nuclear division.[5]
Many eukaryotes are unicellular; the informal grouping called protists includes many of these, with some multicellular forms like the kelps (brown algae). The multicellular eukaryotes include the animals, plants, and fungi.[6] Eukaryotes represent a small minority of the number of organisms, but, as many of them are much larger, their collective global biomass is about equal to that of prokaryotes.[7]
Internal membranes

Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system.[8] Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. 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.[9] Some cell products can leave in a vesicle through exocytosis.[10]
The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow material to move in and out.[11] Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. It includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum.[12] In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.[13]
Vesicles may be specialized; for instance, lysosomes contain digestive enzymes that break down biomolecules in the cytoplasm.[14]
Mitochondria

Mitochondria are organelles found in all but one eukaryote, Monocercomonoides, which has secondarily lost its mitochondria.[15] The mitochondrion is commonly called "the powerhouse of the cell",[16] for its function providing energy by oxidising sugars or fats to produce the energy store ATP.[17][18] Mitochondria have two surrounding membranes, each a phospholipid bi-layer; the inner of which is folded into invaginations called cristae where aerobic respiration takes place.[19]
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.[20]
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.[15] They obtain energy by enzymatic action on nutrients absorbed from the environment. 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. The normal mitochondrial iron-sulfur cluster pathway has been lost secondarily.[15][21]
Plastids

Plants and various groups of algae have plastids as well as mitochondria. Plastids, like mitochondria, have their own DNA and are developed from endosymbionts, in this case cyanobacteria. They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids probably had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion.[22] The capture and sequestering of photosynthetic cells and chloroplasts, kleptoplasty, occurs in many types of modern eukaryotic organisms.[23][24]
Cytoskeletal structures

Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or multiple shorter structures called cilia. These organelles are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin, and are entirely distinct from prokaryotic flagella. They are supported by a bundle of microtubules arising from a centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella may have hairs (mastigonemes), as in many Stramenopiles, and scales connecting membranes and internal rods. Their interior is continuous with the cell's cytoplasm.[25][26]
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. Motor proteins of microtubules, e.g., dynein or kinesin and actin, e.g., myosins provide dynamic character of the network.[27]
Centrioles are often present even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups that give rise to various microtubular roots. 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. Centrioles produce the spindle during nuclear division.[28]
Cell wall
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. The cell wall also prevents over-expansion when water enters the cell.[29]
The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.[30]
Reproduction

Cell division generally takes place asexually by mitosis, a process that allows each daughter nucleus to receive one copy of each chromosome. 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, with two copies of each chromosome in each cell. The diploid phase is formed by fusion of two haploid gametes, such as eggs and spermatozoa, to form a zygote; this may divide by mitosis or undergo chromosome reduction by meiosis.[31] There is considerable variation in this pattern. Plants have both haploid and diploid multicellular phases.[32]
Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times.[33]
The evolution of sexual reproduction may be a primordial and fundamental characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger proposed that facultative sex was present in the common ancestor of all eukaryotes.[34] 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.[35][36] 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.[35][36] Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus Leishmania, have been shown to have a sexual cycle.[37] 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.[38]
History of classification
In antiquity, the two lineages of animals and plants were recognized. They were given the taxonomic rank of Kingdom by Linnaeus in the 18th century. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom.[39] The various single-cell eukaryotes were originally placed with plants or animals when they became known. In 1818, the German biologist Georg A. Goldfuss coined the word protozoa to refer to organisms such as ciliates,[40] and this group was expanded until it encompassed all single-celled eukaryotes, and given their own kingdom, the Protista, by Ernst Haeckel in 1866.[41][42][43] The eukaryotes thus came to be seen as four kingdoms:
The protists were at that time thought to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature.[42] 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.[44]
Internal phylogeny
By 2014, a rough consensus started to emerge from the phylogenomic studies of the previous two decades.[6][45] The majority of eukaryotes can be placed in one of two large clades dubbed Amorphea (similar in composition to the unikont hypothesis) and the Diaphoretickes, which includes plants and most algal lineages. A third major grouping, the Excavata, has been abandoned as a formal group as it is paraphyletic.[46] The proposed 2021 phylogeny below includes only one group of excavates (Discoba), and incorporates the recent proposal that picozoans are close relatives of rhodophytes.[47] The Provora are a group of microbial predators discovered in 2022.[48]
Eukaryotes |
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2200 mya? |
Evolutionary history
Origins
The origin of the eukaryotic cell, also known as eukaryogenesis, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. A number of approaches have been used to find the first eukaryote and their closest relatives. The last eukaryotic common ancestor (LECA) is the hypothetical last common ancestor of all living eukaryotes,[49] and was most likely a biological population.[50] 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.[51] The last common ancestor of 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.[51][52][53]
Eukaryotes differ from prokaryotes in multiple ways, including an endomembrane system and unique biochemical pathways such as sterane synthesis.[54] 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 at that time, but they appear to be universal among eukaryotes. They include the proteins of the cytoskeleton, the complex transcription machinery, the membrane-sorting systems, the nuclear pore, and some enzymes in the biochemical pathways.[55]
Different hypotheses have been proposed as to how eukaryotic cells came into existence. These hypotheses can be classified into two distinct classes – autogenous models and chimeric models.
Autogenous models

Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria.[56] 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. 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.[57]
Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium after a eukaryote with a nucleus has evolved. This theory requires extra assumptions to explain current conditions. For example, as every known eukaryote has a mitochondrion (or at least shows signs of having an ancestor that had), one must assume that any eukaryotic lineages that did not acquire mitochondria became extinct. The theory also does not explain why anaerobic variants of mitochondria have evolved.[58]
Chimeric models
Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. The closest living relatives of these appears to be Asgardarchaeota and (distantly related) the alphaproteobacteria called the proto-mitochondrion. These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell.[59][60]
The inside-out hypothesis
The inside-out hypothesis suggests that 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 in a single phagocytotic event. 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. 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. But eventually the archaeon would engulf the bacteria completely, creating the internal membrane structures and nucleus membrane in the process.[61]
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.[62]
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. 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. This accumulation of beneficial genes gave rise to the genome of the eukaryotic cell, which contained all the genes required for independence.[63][64][65]
The serial endosymbiotic hypothesis

According to serial endosymbiotic theory (championed by Lynn Margulis), a union between a motile anaerobic bacterium (like Spirochaeta) and a thermoacidophilic thermoproteotan (like Thermoplasma which is sulfidogenic in nature) gave rise to the present day eukaryotes. This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. 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. From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alphaproteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. 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 – Desulfobacter and Spirochaeta. However, such an association based on motile symbiosis has never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments. In addition, the theory posits that mitochondrion-less eukaryotes have existed, tying back to the problem in the autogenous model.[56]
The hydrogen hypothesis
In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alphaproteobacterium (the symbiont) gave rise to the eukaryotes. The host used hydrogen (H2) and carbon dioxide (CO2) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and CO2 as byproducts of anaerobic fermentation process. The host's methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation.[66][67][68][69][70]
Endosymbiotic gene transfer acted as a catalyst for the host to acquire the symbionts' carbohydrate metabolism and turn heterotrophic in nature. Subsequently, the host's methane forming capability was lost. Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.[69]
The syntrophy hypothesis
The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this model, the origin of eukaryotic cells was based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a deltaproteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alphaproteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a deltaproteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus, while the deltaproteobacterium contributed towards the cytoplasmic features. This theory incorporates two selective forces at the time of nucleus evolution, namely the presence of metabolic partitioning to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, and the prevention of abnormal protein biosynthesis due to the spread of introns in the archaeal genes after acquiring the mitochondrion and losing methanogenesis.[71][72]
Fossils

The timing of the origin of eukaryotes is hard to determine; Knoll (2006) suggests they developed as much as 2.2 billion years ago. Some acritarchs are known from at least 1.65 billion years ago, and the possible alga Grypania has been found as far back as 2.2 billion years ago.[73] Diskagma has been found in paleosols 2.2 billion years old.[74]
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. Eukaryotic life could have evolved at that time.[75] Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of 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.[76]
The presence of eukaryotic-specific biomarkers (steranes) in Australian shales previously indicated that eukaryotes were present in these rocks dated at 2.7 billion years old,[54][77] which was even 300 million years older than the first geological records of the appreciable amount of molecular oxygen during the Great Oxidation Event. However, these Archaean biomarkers were eventually rebutted as later contaminants.[78] Currently, putatively the oldest biomarker records are only ~800 million years old.[79] In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as 2.3 billion years ago,[80] and thus there is a huge gap between molecular data and geological data, which hinders a reasonable inference of the eukaryotic evolution through biomarker records before 800 million years ago. The nature of steranes as eukaryotic biomarkers is further complicated by the production of sterols by some bacteria.[81][82]
Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive uptick in the zinc composition of marine sediments 800 million years ago has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes, approximately a billion years after their origin (at the latest).[83]
External phylogeny: relationship to Archaea and Bacteria
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. In other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:
- Eukaryotes resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a bacterium, and the nucleus from an archaeon,[84] from a virus,[85][86] or from a pre-cell.[87][88]
- Eukaryotes developed from Archaea, and acquired their bacterial characteristics through the endosymbiosis of a proto-mitochondrion of bacterial origin.[89]
Alternative proposals include:
- 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.[55]
- The last universal common ancestor of the 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.[90]
Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea, and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below, with a modification of hypothesis 2 making the 4th column: The eocyte hypothesis, in which the Archaea are paraphyletic.[91]
1 – Two empires | 2 – Three domains | 3 – Gupta | 4 – Eocyte | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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More recently, researchers have favoured either the three domains (3D)[49][44] or the eocyte hypothesis. A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the Asgard archaea, is:[92][93][94][95][96][97]
Archaea |
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In this scenario, the Asgard group is seen as a sister taxon of the TACK group, which includes Thermoproteota (formerly named eocytes), and Nitrososphaerota (formerly Thaumarchaeota). This group contains many of the eukaryotic signature proteins, and produces vesicles.[98]
In 2017, there was significant pushback against this scenario, arguing that the eukaryotes did not emerge from within the Archaea. Cunha et al. produced analyses supporting the three domains (3D) or Woese hypothesis (2 in the table above) and rejecting the eocyte hypothesis (4 above).[99] 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. They rejected the eocyte hypothesis as the least likely.[100][91] A possible interpretation 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.[90] On the other hand, the researchers who came up with Asgard re-affirmed their hypothesis with additional Asgard samples.[101] Since then, the publication of additional Asgard archaeal genomes and the independent reconstruction of phylogenomic trees by multiple independent laboratories have provided additional support for an Asgard archaeal origin of eukaryotes.
Details of the relation of Asgard archaea and eukaryotes are still under consideration,[102] although, in 2020, it was reported that Candidatus Prometheoarchaeum syntrophicum, a type of cultured Asgard archaea, may be a link between prokaryotes and eukaryotes.[103][98]
See also
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External links

- "Eukaryotes" (Tree of Life Web Project)
- "Eukaryote" at the Encyclopedia of Life
- Attraction and sex among our microbial Last Eukaryotic Common Ancestors, The Atlantic, November 11, 2020