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Eukaryotes
Temporal range: Statherian–Present 1650–0 Ma
Scientific classification Edit this classification
Domain: Eukaryota
(Chatton, 1925) Whittaker & Margulis, 1978
Major subdivisions
Synonyms

The eukaryotes (/juːˈkærioʊts, -əts/)[3] are the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes.

The eukaryotes emerged within the archaeal phylum Promethearchaeota. Ignoring mitochondrial DNA (which is bacterial rather than archaeal), this would imply only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea. Eukaryotes first emerged during the Paleoproterozoic, likely as flagellated cells. The leading evolutionary theory is they were created by symbiogenesis between an anaerobic Promethearchaeota archaeon and an aerobic proteobacterium, which formed the mitochondria. A second episode of symbiogenesis with a cyanobacterium created the plants, with chloroplasts.

Eukaryotic cells contain membrane-bound organelles such as the nucleus, the endoplasmic reticulum, and the Golgi apparatus. Eukaryotes may be either unicellular or multicellular. In comparison, prokaryotes are typically unicellular. Unicellular eukaryotes are sometimes called protists. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion (fertilization).

Etymology

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The word eukaryote is derived from the Greek words "eu" (εὖ) meaning "true" or "good" and "karyon" (κάρυον) meaning "nut" or "kernel", referring to the nucleus of a cell.[4]

Diversity

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Further information: Organism

Eukaryotes are organisms that range from microscopic single cells, such as picozoans under 3 micrometres across,[5] to animals like the blue whale, weighing up to 190 tonnes and measuring up to 33.6 metres (110 ft) long,[6] or plants like the coast redwood, up to 120 metres (390 ft) tall.[7] Many eukaryotes are unicellular; the informal grouping called protists includes many of these, with some multicellular forms like the giant kelp up to 200 feet (61 m) long.[8] The multicellular eukaryotes include the animals, plants, and fungi, but again, these groups too contain many unicellular species.[9] Eukaryotic cells are typically much larger than those of prokaryotes—the bacteria and the archaea—having a volume of around 10,000 times greater.[10][11] Eukaryotes represent a small minority of the number of organisms, but, as many of them are much larger, their collective global biomass (468 gigatons) is far larger than that of prokaryotes (77 gigatons), with plants alone accounting for over 81% of the total biomass of Earth.[12]

The eukaryotes are a diverse lineage, consisting mainly of microscopic organisms.[13] Multicellularity in some form has evolved independently at least 25 times within the eukaryotes.[14][15] Complex multicellular organisms, not counting the aggregation of amoebae to form slime molds, have evolved within only six eukaryotic lineages: animals, symbiomycotan fungi, brown algae, red algae, green algae, and land plants.[16] Eukaryotes are grouped by genomic similarities, so that groups often lack visible shared characteristics.[13]

Distinguishing features

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Further information: Cell (biology) § Eukaryotes

Nucleus

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The defining feature of eukaryotes is that their cells have a well-defined, membrane-bound nucleus, distinguishing them from prokaryotes that lack such a structure. Eukaryotic cells have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton which defines the cell's organization and shape. The nucleus stores the cell's DNA, which is divided into linear bundles called chromosomes;[17] these are separated into two matching sets by a microtubular spindle during nuclear division, in the distinctively eukaryotic process of mitosis.[18]

Biochemistry

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Eukaryotes differ from prokaryotes in multiple ways, with unique biochemical pathways such as sterane synthesis.[19] The eukaryotic signature proteins have no homology to proteins in other domains of life, but 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.[20]

Internal membranes

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Further information: Endomembrane system
Prokaryote, to same scale
Eukaryotic cell with endomembrane system
Eukaryotic cells are some 10,000 times larger than prokaryotic cells by volume, and contain membrane-bound organelles.

Eukaryote cells include a variety of membrane-bound structures, together forming the endomembrane system.[21] 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.[22] Some cell products can leave in a vesicle through exocytosis.[23]

The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow material to move in and out.[24] 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, covered in ribosomes which synthesize proteins; these enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum.[25] In most eukaryotes, these protein-carrying vesicles are released and their contents further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.[26]

Vesicles may be specialized; for instance, lysosomes contain digestive enzymes that break down biomolecules in the cytoplasm.[27]

Mitochondria

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Main article: Mitochondrion
Mitochondria are essentially universal in the eukaryotes, and with their own DNA somewhat resemble prokaryotic cells.

Mitochondria are organelles in eukaryotic cells. The mitochondrion is commonly called "the powerhouse of the cell",[28] for its function providing energy by oxidising sugars or fats to produce the energy-storing molecule ATP.[29][30] Mitochondria have two surrounding membranes, each a phospholipid bilayer, the inner of which is folded into invaginations called cristae where aerobic respiration takes place.[31]

Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, from which it originated, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA.[32]

Some eukaryotes, such as the metamonads Giardia and Trichomonas, and the amoebozoan Pelomyxa, appear to lack mitochondria, but all contain mitochondrion-derived organelles, like hydrogenosomes or mitosomes, having lost their mitochondria secondarily.[33] They obtain energy by enzymatic action in the cytoplasm.[34][33] It is thought that mitochondria developed from prokaryotic cells which became endosymbionts living inside eukaryotes.[35]

Plastids

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Main article: Plastid
The most common type of plastid is the chloroplast, which contains chlorophyll and produces organic compounds by photosynthesis.

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 other eukaryotes through secondary endosymbiosis or ingestion.[36] The capture and sequestering of photosynthetic cells and chloroplasts, kleptoplasty, occurs in many types of modern eukaryotic organisms.[37][38]

Cytoskeletal structures

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Main article: Cytoskeleton
The cytoskeleton. Actin filaments are shown in red, microtubules in green. (The nucleus is in blue.)

The cytoskeleton provides stiffening structure and points of attachment for motor structures that enable the cell to move, change shape, or transport materials. The motor structures are microfilaments of actin and actin-binding proteins. These include α-actinin, fimbrin, and filamin in submembranous cortical layers and bundles. Motor proteins of microtubules, dynein and kinesin, and myosin of actin filaments, make the network dynamic.[39][40]

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. Their interior is continuous with the cell's cytoplasm.[41][42]

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 cytoskeleton, 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.[43]

Cell wall

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Main article: Cell wall

The cells of plants, algae, fungi and most chromalveolates, but not animals, are surrounded by a cell wall. This is 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.[44]

The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked together with hemicellulose, embedded in a pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.[45]

Sexual reproduction

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Further information: Evolution of sexual reproduction
Sexual reproduction requires a life cycle that alternates between a haploid phase, with one copy of each chromosome in the cell, and a diploid phase, with two copies. In eukaryotes, haploid gametes are produced by meiosis; two gametes fuse to form a diploid zygote.

Eukaryotes 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 grow into a body, with its cells dividing by mitosis, and at some stage produce haploid gametes through meiosis, a division that reduces the number of chromosomes and creates genetic variability.[46] There is considerable variation in this pattern. Plants have both haploid and diploid multicellular phases.[47] Eukaryotes have lower metabolic rates and longer generation times than prokaryotes, because they are larger and therefore have a smaller surface area to volume ratio.[48]

The evolution of sexual reproduction may be a primordial characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger have proposed that facultative sex was present in the group's common ancestor.[49] 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.[50][51] Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, core meiotic genes, and hence sex, were likely present in the common ancestor of eukaryotes.[50][51] Species once thought to be asexual, such as Leishmania parasites, have a sexual cycle.[52] Amoebae, previously regarded as asexual, may be anciently sexual; while present-day asexual groups could have arisen recently.[53]

Evolution

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History of classification

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Further information: History of taxonomy

In antiquity, the two lineages of animals and plants were recognized by Aristotle and Theophrastus. The lineages 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.[54] 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,[55] and this group was expanded until Ernst Haeckel made it a kingdom encompassing all single-celled eukaryotes, the Protista, in 1866.[56][57][58] 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.[57] Understanding of the oldest branchings in the tree of life only developed substantially with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, Otto Kandler, and Mark Wheelis in 1990, uniting all the eukaryote kingdoms in the domain "Eucarya", stating, however, that "'eukaryotes' will continue to be an acceptable common synonym".[1][59] In 1996, the evolutionary biologist Lynn Margulis proposed to replace kingdoms and domains with "inclusive" names to create a "symbiosis-based phylogeny", giving the description "Eukarya (symbiosis-derived nucleated organisms)".[2]

Phylogeny

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By the early 21st century, a rough consensus started to emerge from phylogenomic studies.[60][61][62] The majority of eukaryotes can be placed in one of two large clades dubbed Amorphea (similar in composition to the unikont hypothesis) and the Diphoda (formerly bikonts), which includes plants and most algal lineages. A third major grouping, the Excavata, has been abandoned as a formal group as it was found to be paraphyletic.[63] The proposed phylogeny below includes two groups of excavates (Discoba and Metamonada),[64] and incorporates the 2021 proposal that picozoans are close relatives of rhodophytes.[65] The Provora are a group of microbial predators discovered in 2022.[66] TSAR is a possible clade that would contain Telonemia and the SAR supergroup.[67][68][69]

Promethearchaeota
(Asgard archaea)

One view of the great kingdoms and their stem groups.[70][71][72][73][74][75] The Metamonada are hard to place, being sister possibly to Discoba or to Malawimonadida[74] or being a paraphyletic group external to all other eukaryotes.[76] Eukaryotes are thought to have emerged within the archaeal phylum Promethearchaeota.[77][78]

Origin of eukaryotes

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Main article: Eukaryogenesis
In the theory of symbiogenesis, a merger of an archaean and an aerobic bacterium created the eukaryotes, with aerobic mitochondria; a second merger added chloroplasts, creating the green plants.[79]

The origin of the eukaryotic cell, or eukaryogenesis, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The last eukaryotic common ancestor (LECA) is the hypothetical origin of all living eukaryotes,[80] and was most likely a biological population, not a single individual.[81] The LECA is believed to have been a protist with a nucleus, at least one centriole and flagellum, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin or cellulose, and peroxisomes.[82][83][84]

An endosymbiotic union between a motile anaerobic archaean and an aerobic alphaproteobacterium gave rise to the LECA and all eukaryotes with mitochondria. A second, much later endosymbiosis with a cyanobacterium gave rise to the ancestor of plants, with chloroplasts.[79]

The presence of eukaryotic biomarkers in archaea points towards an archaeal origin, except for mitochondrial DNA, which is bacterial in origin. The genomes of Promethearchaeota archaea have plenty of eukaryotic signature protein genes, which play a crucial role in the development of the cytoskeleton and complex cellular structures characteristic of eukaryotes. In 2022, cryo-electron tomography demonstrated that Promethearchaeota archaea have a complex actin-based cytoskeleton, providing the first direct visual evidence of the archaeal ancestry of eukaryotes.[85]

Fossils

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The timing of the origin of eukaryotes is hard to determine, but the discovery of Qingshania magnifica, the earliest multicellular eukaryote from North China which lived 1.635 billion years ago, suggests that the crown group eukaryotes originated from the late Paleoproterozoic (Statherian). The earliest unequivocal unicellular eukaryotes, Tappania plana, Shuiyousphaeridium macroreticulatum, Dictyosphaera macroreticulata, Germinosphaera alveolata, and Valeria lophostriata from North China, lived approximately 1.65 billion years ago.[86]

Some acritarchs are known from at least 1.65 billion years ago, and a fossil, Grypania, which may be an alga, is as much as 2.1 billion years old.[87][88] The "problematic"[89] fossil Diskagma has been found in paleosols 2.2 billion years old.[89]

Reconstruction of the problematic[89] Diskagma buttonii, a terrestrial fossil less than 1mm high, from rocks around 2.2 billion years old

The Neoarchean fossil Thuchomyces shares some similarities with fungi. It especially resembles the problematic fossil Diskagma,[89] with hyphae and multiple differentiated layers.[90] However, it is over 600 million years older than all other possible eukaryotes, and many of its "eukaryote features" are not specific to the clade, meaning it is almost certainly a microbial mat instead.[91]

Structures proposed to represent "large colonial organisms" have been found in the black shales of the Palaeoproterozoic such as the Francevillian B Formation, in Gabon, dubbed the "Francevillian biota" which is dated at 2.1 billion years old.[92][93] However, the status of these structures as fossils is contested, with other authors suggesting that they might represent pseudofossils.[94] The oldest fossils that can unambiguously be assigned to eukaryotes are from the Ruyang Group of China, dating to approximately 1.8-1.6 billion years ago.[95] 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.[96]

The presence of steranes, eukaryotic-specific biomarkers, in Australian shales previously indicated that eukaryotes were present in these rocks dated at 2.7 billion years old,[19][97] but these Archaean biomarkers have been rebutted as later contaminants.[98] The oldest valid biomarker records are only around 800 million years old.[99] In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as 2.3 billion years ago.[100] The nature of steranes as eukaryotic biomarkers is further complicated by the production of sterols by some bacteria.[101][102]

Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive increase 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).[103]

See also

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References

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Revisions and contributorsEdit on WikipediaRead on Wikipedia

Eukaryote

View on Grokipedia
from Grokipedia
Eukaryotes are organisms whose cells contain a membrane-bound that encloses their genetic material in the form of linear chromosomes, along with other membrane-bound organelles that compartmentalize cellular processes. This nuclear envelope, perforated by nuclear pores, separates the DNA from the cytoplasm, enabling complex regulation of gene expression. Unlike , which lack a nucleus and such organelles, eukaryotic cells are typically larger, with dimensions about 10 times greater linearly and 1,000 times greater in volume, supported by a dynamic composed of microtubules, actin filaments, and intermediate filaments. Eukaryotes encompass a broad diversity of life forms, ranging from single-celled to multicellular kingdoms such as , , and . The hallmark organelles of eukaryotic cells include , which generate ATP through oxidative phosphorylation and originated from endosymbiotic ; in photosynthetic eukaryotes, derived from engulfed and responsible for converting sunlight into chemical energy; the , involved in protein and lipid synthesis; and the , which modifies, sorts, and packages molecules for secretion or use within the cell. and handle degradation and metabolic functions, respectively, while the cytoskeleton facilitates intracellular transport, cell division via and , and cellular motility. Eukaryotic genomes are substantially larger and more complex than those of prokaryotes, often containing billions of nucleotide pairs with extensive noncoding DNA that regulates development, particularly in multicellular species. Eukaryotes first appeared approximately 1.6 to 2.2 billion years ago, evolving from an host that engulfed an , leading to the establishment of mitochondria as a defining innovation that boosted energy production and enabled cellular complexity. This endosymbiotic event, supported by evidence such as the prokaryote-like circular DNA and binary fission in mitochondria and chloroplasts, marked a pivotal transition in evolution, allowing for the development of sexual reproduction, larger body sizes, and multicellularity. Modern eukaryotic diversity is organized into several supergroups rather than the traditional four kingdoms (, , , and ), reflecting phylogenetic relationships uncovered through molecular analyses.30257-5) These organisms dominate Earth's biosphere, comprising the majority of biomass and driving key ecological processes like photosynthesis and nutrient cycling.

Fundamentals

Etymology

The term "eukaryote" is derived from the Ancient Greek words eu (εὖ), meaning "true" or "well," and karyon (καρύον), meaning "nut" or "kernel," collectively signifying organisms with a "true kernel" or nucleus. This etymology underscores the defining feature of a membrane-bound nucleus that distinguishes these cells from simpler forms. The term was coined by French biologist Édouard Chatton in his 1925 paper "Pansporella perplex: Reflections on the Biology and Phylogeny of the ," where he first used "eucaryose" (eukaryote) to describe nucleated cells in contrast to non-nucleated ones. Chatton later elaborated on this distinction in his 1937 work, formalizing the dichotomy between eucaryotes and procaryotes (prokaryotes). Prior to Chatton's introduction, German biologist had proposed the term "" in 1866 within his Generelle Morphologie der Organismen to classify primitive, structureless, non-nucleated organisms as a basal group in his . In early 20th-century cytology, Chatton's terminology built upon and refined this framework, elevating the distinction to highlight the fundamental morphological divide between nucleated cells (eukaryotes) and bacteria-like forms previously grouped under . This in facilitated clearer in microbial studies, contrasting eukaryotes with prokaryotes as non-nucleated cells.

Definition

Eukaryotes comprise one of the three domains of life, Eukarya, alongside the domains and ; they are defined by cells that possess a membrane-bound nucleus enclosing the genetic material and typically feature an array of membrane-bound organelles that compartmentalize cellular functions. The name "eukaryote" originates from the Greek terms eu (true) and karyon (kernel), reflecting the presence of a distinct, membrane-enclosed nucleus. Eukaryotic cells generally range from 10 to 100 μm in diameter, though extremes exist across the domain; the smallest known free-living eukaryote, the marine alga Ostreococcus tauri, measures approximately 0.8 μm, while the largest recorded eukaryotic cell, the ovum of the ostrich (Struthio camelus), reaches up to 15 cm in length. Eukaryotes include both unicellular organisms, such as protists, and multicellular forms that make up the kingdoms Animalia, Plantae, and Fungi. A 2011 estimate suggests 8.7 million eukaryotic inhabit , with roughly 86% yet to be described. Characteristic features of eukaryotic cells encompass multiple linear chromosomes organized within the nucleus, larger 80S ribosomes responsible for protein synthesis, and plasma membranes enriched with sterols like cholesterol that contribute to membrane fluidity and stability.

Distinguishing Features

Nucleus

The nucleus is the defining organelle of eukaryotic cells, serving as the primary site for storing genetic information, regulating gene expression, and coordinating cellular activities. It houses the cell's genome in the form of chromatin, a complex of DNA and proteins, and facilitates processes such as DNA replication, RNA transcription, and RNA processing. Unlike the prokaryotic nucleoid, which is an unenclosed region of DNA in the cytoplasm, the eukaryotic nucleus is a membrane-bound compartment that allows for spatial separation of transcription and translation, enabling more sophisticated control over gene expression. The , a double-membrane structure continuous with the , encloses the nucleus and separates its contents from the . This envelope is perforated by thousands of nuclear pore complexes (NPCs), large protein assemblies that mediate selective transport between the nucleus and . Each NPC, composed of approximately 30 different nucleoporins forming a cylindrical channel about 120 nm in , permits the passive of small molecules (less than 40 kDa) while actively transporting larger macromolecules, such as proteins and RNAs, via karyopherin receptors and the Ran system. This regulated transport is essential for delivering transcription factors to the nucleus and exporting mature mRNAs, thereby controlling gene regulation. Within the nucleus, chromatin is organized into discrete chromosomes, with DNA tightly packaged around histone proteins to form nucleosomes, which further coil into higher-order structures. This organization compacts the eukaryotic genome, which is typically much larger than prokaryotic ones—ranging from about 10 Mb in some yeasts to over 100 Gb in certain plants and amphibians, often encoding thousands to tens of thousands of genes compared to the 1,000–10,000 genes in bacterial genomes of 1–10 Mb. The nucleolus, a prominent substructure, is the site of ribosomal RNA (rRNA) synthesis and ribosome subunit assembly, involving the transcription of rRNA genes by RNA polymerase I and the processing of pre-rRNA into mature forms. Variations in occur across eukaryotes; for instance, some fungi and multinucleate cells like muscle fibers form syncytia with multiple nuclei sharing a common , allowing coordinated but independent nuclear functions. In contrast, mature mammalian red blood cells extrude their nucleus during development, becoming enucleate to maximize space for and enhance oxygen transport. These adaptations highlight the nucleus's role in supporting diverse eukaryotic lifestyles while maintaining its core functions in management and cellular control.

Biochemistry

Eukaryotic genomes are characteristically larger than those of prokaryotes, often spanning several orders of magnitude in size, from about 10 megabases in to over 100 gigabases in some amphibians and , primarily due to the expansion of non-coding regions including introns. Unlike prokaryotic genes, which are typically continuous, eukaryotic genes are organized into exons separated by introns, non-coding sequences that are transcribed into pre-mRNA but removed through a process called splicing to produce mature mRNA. This splicing mechanism, mediated by the , allows for , enabling a single to produce multiple protein isoforms and increasing proteomic diversity.30297-3) Additionally, eukaryotic is packaged with histones, and modifications such as and on these histones play crucial roles in epigenetic regulation, influencing without altering the DNA sequence. Eukaryotic cell membranes incorporate sterols, such as in animals, in fungi, and phytosterols (e.g., sitosterol and ) in , which are absent in most prokaryotes and essential for maintaining , permeability, and the formation of lipid rafts. These sterols intercalate between phospholipids, modulating the packing of tails and preventing phase transitions that could rigidify the at physiological temperatures.72353-0) Prokaryotes, in contrast, rely on for similar functions, highlighting a key biochemical divergence. Eukaryotes also synthesize unique like , which are major components of plasma membranes and contribute to signaling, trafficking, and barrier functions in these cells.00107-8) Metabolic pathways in eukaryotes show compartmentalization distinct from prokaryotes; for instance, occurs in the across both domains, generating pyruvate and ATP anaerobically. However, eukaryotes perform the Krebs cycle (tricarboxylic acid cycle) within mitochondria, oxidizing to produce reducing equivalents for further harvest, a feature not compartmentalized similarly in prokaryotes. Eukaryotic-specific enzymes, such as , further differentiate carbohydrate storage; this enzyme requires a primer chain for activity and is regulated by , unlike prokaryotic counterparts that initiate synthesis de novo. Protein synthesis in eukaryotes utilizes ribosomes in the , larger and more complex than the 70S ribosomes of prokaryotes, with distinct ribosomal RNAs and proteins that enable higher fidelity and regulation. Many eukaryotic proteins destined for organelles or secretion feature N-terminal signal peptides that direct nascent polypeptides to specific targeting machinery, such as the for insertion, ensuring proper subcellular localization.

Endomembrane System

The is a complex network of membrane-bound organelles and vesicles in eukaryotic cells that facilitates the synthesis, modification, sorting, and transport of proteins and , ensuring proper cellular function and communication. This system is unique to eukaryotes and plays a central role in compartmentalizing cellular processes, which contrasts with the lack of such organized internal membranes in prokaryotes. Key components of the endomembrane system include the (ER), Golgi apparatus, lysosomes, and vacuoles. The ER is divided into rough and smooth regions: the rough ER, studded with ribosomes, is primarily responsible for protein synthesis and folding, while the smooth ER handles synthesis, detoxification, and calcium storage. Proteins synthesized in the rough ER are translocated into its lumen for initial , whereas are assembled in the smooth ER membranes. The Golgi apparatus receives these products via vesicular transport and modifies them through further , sulfation, and proteolytic processing before sorting them to their destinations. Lysosomes function as digestive compartments containing hydrolytic enzymes that degrade macromolecules from or , while in and fungi, vacuoles serve analogous roles in storage, degradation, and maintaining . Vesicular transport within the relies on coated vesicles that mediate the movement of cargo between organelles. COPII-coated vesicles bud from the ER to transport newly synthesized proteins to the Golgi, while COPI-coated vesicles facilitate retrograde transport from the Golgi back to the ER and intra-Golgi trafficking. pathways, such as clathrin-mediated uptake at the plasma membrane, internalize extracellular materials into endosomes, which can mature into lysosomes or recycle components back to the surface. , conversely, delivers secretory vesicles to the plasma membrane for release of hormones, enzymes, or matrix components.30153-0) The primary functions of the encompass the secretory pathway, which directs proteins and from synthesis to or integration, and membrane recycling, which maintains and protein through and vesicle fusion. This dynamic system enables eukaryotes to secrete large volumes of material and respond to environmental cues, capabilities that are rudimentary or absent in prokaryotes due to their simpler architecture. The is continuous with the ER as a domain, allowing shared composition and selective transport. Variations in the occur across eukaryotic lineages; for instance, cells typically feature compact Golgi stacks with 4-6 cisternae, whereas cells exhibit more dispersed, larger Golgi stacks (up to 20 cisternae per unit) adapted for high-volume secretion of cell wall . These structural differences reflect adaptations to diverse physiological demands, such as rapid growth in .

Mitochondria

Mitochondria are double--bound organelles found in nearly all eukaryotic cells, characterized by an outer that is smooth and permeable and an inner folded into structures known as cristae to increase surface area for energy production. The space enclosed by the inner membrane, called , contains a circular known as (mtDNA), which is typically 16–18 kb in size in animals and encodes a small number of proteins essential for mitochondrial function. Additionally, houses 70S ribosomes, similar to those in , which facilitate the of mtDNA-encoded genes. The primary function of mitochondria in eukaryotes is to generate (ATP) through , a process that occurs along the inner membrane. This involves the , consisting of four protein complexes (I–IV), which transfer electrons from NADH and FADH₂ to oxygen, creating a proton that drives to produce ATP from ADP and inorganic . The overall simplified reaction for this process is: ADP+Pi+NADH+12O2→ATP+NAD++H2O\text{ADP} + \text{P}_\text{i} + \text{NADH} + \frac{1}{2}\text{O}_2 \rightarrow \text{ATP} + \text{NAD}^+ + \text{H}_2\text{O} Beyond energy production, mitochondria play a key role in () by releasing from the intermembrane space into the , which activates and initiates the apoptotic cascade. Mitochondrial inheritance is predominantly maternal in most animals and , as mitochondria are typically degraded after fertilization, ensuring transmission through the egg . The number of mitochondria per eukaryotic cell varies widely, from hundreds in small cells to thousands in high-energy-demand tissues like muscle or liver, reflecting the cell's metabolic needs. However, some anaerobic eukaryotes, such as the parasite Giardia lamblia, lack typical mitochondria and instead possess highly reduced organelles called mitosomes that do not produce ATP. This structural and functional diversity underscores the endosymbiotic origin of mitochondria from ancient integrated into early eukaryotic hosts.

Plastids

Plastids are double-membrane-bound organelles found in the cells of plants and algae, originating from primary or secondary endosymbiosis events involving . These organelles perform diverse functions depending on their type, including , storage of and pigments, and synthesis of various metabolites essential for eukaryotic cellular metabolism. The primary types of plastids include chloroplasts, which are specialized for and contain green pigments; amyloplasts, responsible for storage in non-photosynthetic tissues such as roots and tubers; chromoplasts, which accumulate colorful pigments like to aid in and in flowers and fruits; and leucoplasts, colorless plastids that store , proteins, or in underground or internal plant parts. Chloroplasts, the most studied plastid type, consist of an outer and inner envelope membrane enclosing the stroma, a fluid matrix, and a network of membranes stacked into grana where occur. The chloroplast genome, known as cpDNA, is a circular typically ranging from 120 to 160 kilobases in size, encoding about 100–200 genes for proteins involved in and . In chloroplasts, photosynthesis proceeds in two main stages: the light-dependent reactions in the thylakoid membranes, where pigments such as chlorophyll a, chlorophyll b, and absorb light energy to split water molecules, releasing oxygen and generating ATP and NADPH; and the light-independent Calvin cycle in the stroma, where CO₂ is fixed into glucose using the ATP and NADPH produced. The overall equation for photosynthesis is: 6CO2+6H2O+light energy→C6H12O6+6O26CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2 and b primarily capture blue and red wavelengths of light, while like and protect against excess light and assist in energy transfer. The , occurring in the stroma, involves enzymes such as to carboxylate ribulose-1,5-bisphosphate, leading to the production of glyceraldehyde-3-phosphate, a precursor to glucose. Plastids are distributed across photosynthetic eukaryotes, including all and many algal groups such as and , where they enable autotrophic nutrition; however, they are absent in heterotrophic eukaryotes like animals and fungi. Leucoplasts, a subset of non-green plastids, predominate in tissues for storage functions, highlighting the plasticity of these organelles in adapting to specific cellular needs.

Cytoskeleton

The eukaryotic cytoskeleton is a dynamic network of protein filaments and associated motor proteins that maintains cell shape, facilitates intracellular transport, enables motility, and drives cell division. Unlike the simpler cytoskeletal elements in prokaryotes, such as FtsZ and MreB homologs, the eukaryotic version is more complex, featuring three distinct filament systems—microtubules, actin microfilaments, and intermediate filaments—along with diverse accessory proteins and ATP-powered motors that allow for rapid remodeling through polymerization and depolymerization. This complexity supports advanced eukaryotic functions, including mitosis and phagocytosis, and recent discoveries indicate pre-eukaryotic origins, with actin homologs identified in Asgard archaea like Candidatus Prometheoarchaeum syntrophicum. Microtubules, with a of approximately 25 nm, are hollow polymers composed of α- and β-tubulin heterodimers arranged into 13 protofilaments, forming polarized structures with dynamic plus and minus ends. They serve as tracks for intracellular transport, form the mitotic spindle during to segregate chromosomes, and contribute to and shape maintenance. microfilaments, or F-actin, are thinner at about 7 nm and consist of globular G-actin monomers that assemble into double-helical filaments, enabling contractility in processes like and through structures such as lamellipodia and . Intermediate filaments, roughly 10 nm in diameter, are rope-like assemblies of diverse proteins including keratins in epithelial cells, in mesenchymal cells, and in the ; they provide mechanical resilience, resist tensile stress, and anchor organelles like the nucleus. Motor proteins harness to generate force and movement along these filaments. Kinesins typically walk toward the microtubule plus end, transporting vesicles, mitochondria, and other cargoes outward from the cell center, while dyneins move toward the minus end, facilitating inward transport and powering the beating of cilia and flagella. Myosins interact with filaments, with myosin II driving bipolar sliding for and , and unconventional myosins like myosin V enabling short-range transport and membrane tethering. These motors, absent in prokaryotes, enable precise intracellular trafficking, including positioning, and support by coordinating cytoskeletal dynamics with adhesion sites. The eukaryotic cytoskeleton's ability to undergo rapid assembly and disassembly, regulated by nucleotide and accessory proteins, underpins its roles in responding to environmental cues and maintaining cellular integrity.

Cell Wall

Eukaryotic cells exhibit diverse extracellular structures, with cell walls present in many but absent in animals, where reliance on internal cytoskeletal elements and extracellular matrices suffices for support. In contrast to prokaryotes, eukaryotic cell walls lack , a defining component of bacterial cell envelopes that provides rigidity through cross-linked and peptides. This absence distinguishes eukaryotic barriers, which instead utilize like , , or silica tailored to specific lineages. For instance, cells and feature walls primarily composed of microfibrils embedded in a matrix of hemicelluloses (such as xyloglucans) and pectins, forming a flexible yet robust . Fungal walls consist mainly of (10-40%) intertwined with β-glucans, creating a layered that varies by species, while diatoms—a group of unicellular —employ silica to form intricate, porous frustules. These materials enable group-specific adaptations, such as the sulfated (e.g., alginates in ) that confer gel-like properties for marine environments. The structure of eukaryotic cell walls typically forms a porous matrix that encases the plasma membrane, providing mechanical strength and protection against environmental stresses while permitting nutrient exchange. In , primary walls are thin and dynamic, allowing cell expansion during growth, whereas secondary walls incorporate for added rigidity in supportive tissues. This matrix regulates by countering —the internal hydrostatic force generated by influx—that maintains cell shape and drives expansion; without the wall, excessive swelling could occur. Functions extend to pathogen defense, where wall components like pectins release elicitors (e.g., oligogalacturonides) upon degradation, triggering immune responses. Walls also interact briefly with the , anchoring filaments to enhance overall rigidity during deformation. In protists, variations include a —a diffuse layer serving as a protective analogous to a simplified wall, aiding in and evasion of predators. Cell walls are dynamic structures that remodel during growth and development, particularly in processes like tip growth observed in pollen tubes, where localized secretion of wall materials at the apex balances turgor-driven extension to achieve rapid elongation rates exceeding 1 cm/h. Enzymes such as methylesterases and expansins transiently loosen the matrix, facilitating insertion of new without compromising integrity. In fungi, synthases enable polar extension in hyphae, mirroring this adaptability. These mechanisms underscore the wall's role not merely as a static barrier but as an active participant in cellular across eukaryotic diversity.

Reproduction

Eukaryotes reproduce through both asexual and sexual mechanisms, allowing for rapid population growth or depending on environmental conditions. Asexual reproduction is prevalent in unicellular eukaryotes and involves processes that produce genetically identical offspring without fusion. Common methods include binary fission, where a single cell divides into two daughter cells after and , as seen in protists like amoebae. occurs when a small outgrowth forms on the parent cell, developing into a new that detaches, such as in yeasts. Fragmentation involves the breaking of the parent body into pieces, each of which regenerates into a complete individual, typical in some and fungi. Sexual reproduction in eukaryotes is characterized by meiosis, which reduces the chromosome number from diploid to haploid to produce gametes, followed by syngamy, the fusion of these gametes to restore the diploid state. This process introduces genetic variation through meiosis and fertilization. In many multicellular eukaryotes, particularly plants and algae, sexual reproduction features an alternation of generations, where a haploid gametophyte phase produces gametes via mitosis, and the resulting diploid zygote develops into a sporophyte phase that undergoes meiosis to produce haploid spores. The nucleus plays a key role in gamete formation by housing the genetic material that undergoes meiotic division. A distinctive feature of eukaryotic sexual reproduction is genetic recombination, primarily achieved through crossing over during prophase I of meiosis, where homologous chromosomes exchange segments of DNA, shuffling alleles and increasing diversity. In animals, prevails, with males producing numerous small, motile and females producing fewer large, nutrient-rich eggs, reflecting an evolutionary divergence in gamete investment. Variations on these reproductive strategies exist, such as in certain animals, where females develop offspring from unfertilized eggs, producing clones without male contribution, as observed in some reptiles and . In plants, allows asexual seed production, bypassing and fertilization to yield embryos genetically identical to the mother, common in some angiosperms.

Diversity

Overview

Eukaryotes represent one of the most diverse groups of organisms on , with an estimated total of 8.7 million , of which approximately 2 million have been described as of , leaving about 77% undescribed. This vast array spans unicellular protists, such as amoebae and , to highly complex multicellular forms organized into kingdoms including Animalia, Plantae, and Fungi. Distinguished by features like a membrane-bound nucleus and organelles that enable intricate cellular processes, eukaryotes underpin much of life's complexity. Eukaryotes inhabit nearly every conceivable environment, thriving ubiquitously in , soils, freshwater systems, and even airborne as spores or aerosols. They fulfill essential ecological roles, acting as primary producers via photosynthetic that contribute roughly 50% of global atmospheric oxygen production, as decomposers that recycle nutrients through fungal activity, and as predators that regulate populations in food webs. In terms of size and morphology, eukaryotes display extraordinary variation, ranging from minute unicellular parasites and free-living cells around 0.8–1 μm in diameter, such as Ostreococcus tauri, to enormous multicellular entities like giant kelp (), which can extend up to 60 meters in length. Symbiotic relationships are common, as seen in lichens formed by fungi and photosynthetic partners like , enhancing survival in harsh conditions. Eukaryotes exert significant economic and medical influences on human society. Multicellular plants supply critical crops that form the basis of global agriculture, supporting food security for billions. Certain protists, including Plasmodium species, cause debilitating diseases like malaria, which led to an estimated 263 million cases and 597,000 deaths in 2023. Additionally, algae hold promise for biofuels, with potential U.S. production capacity estimated at 152 million tons of biomass per year to advance renewable energy.

Major Groups

Eukaryotes are broadly classified into several major groups, including the kingdoms Animalia, Plantae, and Fungi, as well as the paraphyletic assemblage of protists and other distinct lineages such as , , and the recently identified supergroup Provora. These groups encompass a vast range of forms, from unicellular microbes to complex multicellular organisms, reflecting the diversity within the domain Eukarya. While traditional kingdom-level classifications provide a foundational framework, modern understandings recognize supergroups based on molecular and morphological evidence, highlighting the non-monophyletic nature of some categories like protists. The kingdom Animalia consists of multicellular, heterotrophic organisms that obtain nutrients by ingesting other organisms and are characterized by in at least one life stage, often with specialized tissues and organ systems. Approximately 1.5 million of animals have been described, predominantly , making Animalia the most species-rich eukaryotic kingdom. In contrast, the kingdom Plantae includes multicellular, autotrophic that perform using chloroplasts, typically featuring cell walls of and in their life cycles. Around 390,000 plant are known, encompassing vascular plants like flowering plants and non-vascular forms such as mosses. The kingdom Fungi comprises primarily multicellular, heterotrophic organisms that absorb nutrients from their environment, with chitinous cell walls and roles as decomposers, symbionts, or pathogens; about 140,000 fungal have been described, though estimates suggest millions more await discovery. Protists represent a paraphyletic collection of mostly unicellular or simple multicellular eukaryotes that do not fit into the other kingdoms, encompassing a wide array of free-living, photosynthetic, or heterotrophic forms. Key subgroups include the , such as dinoflagellates, which are often photosynthetic or parasitic protists with characteristic alveolar sacs beneath their cell membranes, and the stramenopiles, featuring organisms like that possess flagella with tubular hairs and are major contributors to . Additional major lineages include , which are amoeboid protists known for pseudopod-based locomotion and encompassing slime molds that exhibit both unicellular and multicellular stages during their life cycles, and , a diverse group including , shelled that form intricate tests used in paleoceanography. In 2022, the supergroup Provora was established as a novel lineage of microbial predators, comprising small, voracious flagellates that actively hunt and other microbes through nibbling behavior, distinct genetically and morphologically from other eukaryotes. Certain eukaryotic lineages illustrate transitional forms between unicellularity and multicellularity, such as colonial in the Volvocaceae family. For instance, species form spherical colonies of thousands of biflagellated cells connected by cytoplasmic bridges, where specialized somatic and reproductive cells emerge, representing a step toward division of labor seen in more complex multicellularity. These colonial structures bridge the gap from solitary unicellular ancestors like to fully integrated multicellular organisms, providing insights into early evolutionary innovations in eukaryote complexity.

Classification and Phylogeny

History of Classification

The classification of eukaryotes has evolved significantly since the 18th century, beginning with simple dichotomies that grouped all life into broad categories based on observable traits. In 1758, proposed a two-kingdom system in his , dividing living organisms into the kingdoms Plantae, encompassing sessile, photosynthetic entities including , and Animalia, comprising motile forms. This framework reflected the limited understanding of cellular differences at the time, placing diverse eukaryotes like and fungi under Plantae due to superficial resemblances such as immobility and lack of locomotion. By the mid-19th century, the recognition of unicellular organisms prompted refinements to accommodate microscopic life. In 1866, introduced the kingdom Protista in his Generelle Morphologie der Organismen to classify primitive, unicellular eukaryotes such as and separately from multicellular and animals, drawing on evolutionary ideas from Darwin to emphasize their foundational role in life's hierarchy. However, challenges persisted in eukaryotic ; algae were traditionally subsumed within Plantae for their photosynthetic capabilities, while fungi, initially grouped with due to their sessile nature, faced reclassification in the 1890s as mycologists highlighted differences in nutrition and reproduction. Anton de Bary's 1887 work, Comparative Morphology and Biology of the Fungi, Mycetozoa and Bacteria, played a pivotal role by demonstrating fungi's absorptive heterotrophy and distinct life cycles, paving the way for their separation from the plant kingdom. The 20th century brought more structured systems incorporating cellular organization. In 1969, Robert Whittaker proposed a five-kingdom classification in his seminal paper "New Concepts of Kingdoms of Organisms," delineating (prokaryotes), Protista (unicellular eukaryotes), Fungi (absorptive heterotrophs), Plantae (multicellular photosynthetic autotrophs), and Animalia (multicellular motile heterotrophs), which resolved prior ambiguities by emphasizing eukaryotic distinctions like nuclear membranes and organelle complexity. This system gained widespread adoption in biology education and research for its balance of morphological and physiological criteria. The advent of molecular techniques revolutionized eukaryotic classification in the late . In 1990, and colleagues, using (rRNA) sequencing, established the three-domain system in their PNAS paper "Towards a Natural System of Organisms," positioning Eukarya as a distinct domain alongside and based on deep genetic divergences, thereby elevating eukaryotes from a kingdom within broader schemes to a fundamental branch of life. This shift marked the transition from phenotype-driven to phylogeny-informed , addressing longstanding issues in grouping diverse eukaryotic lineages.

Modern Phylogeny

The modern phylogeny of eukaryotes is primarily reconstructed using phylogenomic approaches, which analyze large datasets of multiple genes (often hundreds) from diverse taxa to infer evolutionary relationships, complemented by analyses of rare genomic changes such as gene fusions, insertions, or synteny patterns that occur infrequently and thus provide strong phylogenetic signals. These methods have supplanted earlier morphology-based classifications, revealing a tree of life divided into approximately nine major supergroups that encompass all eukaryotic diversity. A foundational dichotomy in eukaryotic phylogeny contrasts the supergroup Amorphea—encompassing Amoebozoa and Opisthokonta (the latter including animals, fungi, and their relatives)—with other lineages formerly grouped as Bikonta, which include plants, excavates, and the SAR clade; however, the Bikonta hypothesis has been largely abandoned in favor of more nuanced groupings based on genomic evidence. Amorphea, often referred to as the unikonts in older literature, is characterized by shared traits like a single posterior flagellum in motile forms and specific molecular synapomorphies. The remaining diversity falls into several supergroups, including Excavata (a diverse assemblage of often anaerobic or parasitic protists like diplomonads and parabasalids), Diaphoretickes (featuring Archaeplastida, the photosynthetic lineage containing plants, green algae, red algae, and glaucophytes), and SAR (comprising Stramenopiles such as diatoms and oomycetes, Alveolates including ciliates and apicomplexans, and Rhizaria like foraminiferans). Additional supergroups include Haptista (haptophytes and centrohelids), Cryptista, and CRuMs (a clade of amoeboid protists). Recent discoveries have refined these supergroups through single-cell and expanded phylogenomic datasets. In 2021, picozoans—small, plastid-lacking —were shown to be close relatives of within , highlighting secondary loss of photosynthetic organelles and aiding resolution of internal branching in this group. The 2022 description of Provora as a novel predatory supergroup introduced a distinct lineage of small, flagellated microbial predators that "nibble" prey using extrusomes, branching deeply near the eukaryotic root based on 320-protein analyses and morphologically distinct from other groups. Subsequent studies, including phylogenomic analyses up to 2025, have placed Provora within a new supergroup that also encompasses Hemimastigophorans and , further resolving deep eukaryotic branching. These additions contribute to the recognition of approximately nine major supergroups as of 2025, with ongoing refinements from metagenomic surveys uncovering hidden diversity. The position of the eukaryotic root remains debated, with phylogenomic studies split between a root between Opisthokonta/Amorphea and the rest of eukaryotes (supporting an early divergence of animal-fungal lineages) versus a neomuran root placing the last eukaryotic common ancestor as sister to Asgard archaea within a broader archaeal radiation. Asgard archaea, discovered in 2015 and expanded since, represent the closest prokaryotic relatives to eukaryotes, sharing genes for eukaryotic signature proteins like actin and tubulin that likely facilitated the evolution of complex cells. Multigene supermatrices and rare genomic changes continue to inform this debate, with recent analyses favoring an excavate-rooted tree in some datasets.

Evolution

Origins

The emergence of eukaryotic cells is hypothesized to have occurred approximately 2.0 to 1.8 billion years ago, coinciding with the (GOE), a period of rising atmospheric oxygen levels around 2.4 to 2.2 billion years ago that likely facilitated the metabolic transitions necessary for complex cellular life. The last eukaryotic common ancestor (LECA) is reconstructed as possessing key features such as a nucleus, , and , indicating that these innovations were established prior to the diversification of major eukaryotic lineages. Molecular clock analyses support this timeline, placing LECA's origin in the late era, after the GOE had begun to reshape Earth's geochemical environment and enable oxygen-dependent processes. Current models posit that eukaryotes arose from a fusion between a host cell from the Asgard superphylum of archaea and an alphaproteobacterium, which later became the mitochondrial ancestor. The Asgard archaea, identified through metagenomic studies, share extensive genetic inventory with eukaryotes, including genes for eukaryotic signature proteins involved in membrane remodeling and signaling. A pivotal model organism in this context is Promethearchaeum syntrophicum from the Promethearchaeota phylum (formerly grouped under Asgard), isolated in 2020; its genome encodes actin-like proteins and demonstrates primitive phagocytic capabilities, suggesting that the archaeal host could engulf bacterial partners through membrane invaginations, a precursor to eukaryotic engulfment. Key innovations during this prokaryotic fusion included the formation of the , likely through the fusion of intracellular vesicles derived from the archaeal plasma membrane, creating a double-membrane barrier that compartmentalized genetic material. Concurrently, extensive gene transfer occurred, with thousands of alphaproteobacterial escaping to the host nucleus, enabling coordinated regulation of mitochondrial function and contributing to the genetic complexity of LECA.01394-2) This relocation, driven by endosymbiotic integration, reduced redundancy and optimized energy metabolism within the emerging eukaryotic cell.01394-2) Debates persist regarding the metabolic drivers of eukaryogenesis, particularly between the hydrogen hypothesis and alternative synthase-focused models. The hydrogen hypothesis proposes that the symbiosis was initiated by a syntrophic relationship, where the archaeal host, dependent on for , partnered with a hydrogen-producing alphaproteobacterium, fostering interdependence and eventual integration. In contrast, synthase-first perspectives emphasize the primacy of acquisition from the bacterial partner, arguing that enhanced bioenergetic efficiency via proton gradients, rather than transfer, was the initial selective force enabling cellular complexity in an oxygenated post-GOE world. These hypotheses highlight ongoing discussions about whether anaerobic syntrophy or aerobic harnessing predominated in the transition to eukaryotic .

Endosymbiosis

The endosymbiotic theory posits that key eukaryotic organelles, particularly and plastids, originated through a series of endosymbiotic events involving the engulfment of prokaryotic cells by a host eukaryote or proto-eukaryote. This process, known as serial endosymbiosis, began with the incorporation of an alphaproteobacterium that evolved into the approximately 1.5–2 billion years ago, providing the host with efficient aerobic respiration capabilities. Subsequent endosymbiosis involved the uptake of a cyanobacterium by a photosynthetic eukaryote ancestor, giving rise to primary plastids in the supergroup (including glaucophytes, , and /) around 1–1.5 billion years ago. In other eukaryotic lineages, secondary and tertiary endosymbioses occurred, where heterotrophic eukaryotes engulfed photosynthetic eukaryotes, leading to plastids in groups like stramenopiles, , and euglenids, with further complexity in dinoflagellates and cryptophytes. Compelling evidence supports these endosymbiotic origins. Organelle genomes exhibit bacterial-like features, such as circular DNA, their own ribosomes, and gene sequences phylogenetically closest to for mitochondria and for plastids. Both s are bounded by double membranes, interpreted as the inner membrane from the endosymbiont's plasma membrane and the outer from the host's phagosomal membrane formed during engulfment. Additionally, sophisticated protein import machinery allows nuclear-encoded proteins—targeted via N-terminal presequences for mitochondria or transit peptides for plastids—to be translocated across these membranes, a system absent in free-living prokaryotes but essential for function. The evolutionary process involved initial phagocytic engulfment without immediate digestion, followed by metabolic integration and extensive gene transfer from the endosymbiont to the host nucleus. In mitochondria, for instance, only about 10–13 genes remain in the organelle genome, with roughly 90% of the original ~1,000–2,000 bacterial genes relocated to the nucleus, where they are expressed and the proteins imported back. This transfer likely occurred gradually, driven by selective advantages like reduced rates in the nucleus and coordinated of . The proposes that the alphaproteobacterial endosymbiont was retained because it produced , which the anaerobic archaeal-like host used as an source via hydrogen-dependent enzymes, fostering a syntrophic relationship that stabilized the . More complex endosymbiotic derivatives illustrate ongoing evolutionary dynamics. Kleptoplasty, observed in sacoglossan sea slugs like Elysia chlorotica, involves the temporary sequestration of functional chloroplasts from ingested algae, allowing the host to perform photosynthesis for weeks to months without algal nuclear genes, though lacking permanent integration. In apicomplexan parasites such as Plasmodium falciparum, the apicoplast—a non-photosynthetic plastid remnant—originated from a secondary endosymbiosis of a red alga, retaining roles in fatty acid and isoprenoid biosynthesis despite extensive gene loss and nuclear relocation.00025-6) These cases highlight how endosymbiosis can lead to diverse organelle fates, from full integration to transient or modified retention.

Fossil Record

The fossil record of eukaryotes is primarily preserved through biomarkers and body fossils, providing evidence of their emergence and diversification over billions of years. The oldest undisputed eukaryotic biomarkers are steranes derived from eukaryotic s, identified in the 1.64 billion-year-old (Ga) Barney Creek Formation of the McArthur Basin in . These molecular fossils indicate the presence of oxygen-dependent eukaryotic biosynthesis during the , aligning with rising atmospheric oxygen levels that facilitated sterol production. Earlier claims of steranes in 2.7 Ga rocks from the in , initially reported as evidence for ancient eukaryotes, have been reappraised and attributed to modern contaminants introduced during sample handling or storage. Body fossils offer direct morphological evidence, beginning with possible eukaryotic forms in the late Paleoproterozoic. Grypania spiralis, a coiled, macroscopic filament up to several centimeters long, occurs in the ~1.89 Ga Negaunee Iron Formation of , , and is interpreted as an early eukaryotic alga based on its size, spiral morphology, and inferred photosynthetic habit. Slightly younger assemblages include organic-walled microfossils known as acritarchs, such as Tappania plana from the 1.64 Ga Chuanlinggou Formation in , which exhibit complex features like irregular tubular processes and a distinct neck-like extension indicative of eukaryotic cellular organization and cytoskeletal capabilities. From the same formation, multicellular filaments identified as Qingshania magnifica, dated to approximately 1.635 Ga, represent early eukaryotic with , indicating simple multicellularity arose earlier than previously recognized. These acritarchs represent a diversification of unicellular eukaryotes between 1.8 and 1.6 Ga. Evidence for multicellularity appears later in the . Bangiomorpha pubescens, a filamentous red alga from the ~1.2 Ga Hunting Formation on Somerset Island, , shows differentiated cells, apical growth, and structures suggestive of , marking the earliest record of crown-group multicellular eukaryotes. In the , phosphatized microfossils from the 635 Ma Doushantuo Formation in include embryo-like forms with cleavage stages and spheroidal shapes, interpreted as early animal embryos preserved in exceptional Lagerstätten. Significant gaps persist in the eukaryotic record due to the poor preservation potential of soft-bodied, non-mineralizing forms in pre-Ediacaran sediments, where diagenetic alteration and metamorphism often obscure delicate structures. analyses, calibrated with these fossils, suggest that major eukaryotic lineages diverged earlier than the oldest preserved evidence, potentially by 1.8–1.5 Ga, highlighting a rather than a true absence of earlier forms; this timeline loosely aligns with endosymbiotic events inferred from origins.

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