Eocyte hypothesis

Last updated

Karyota
Urzwerg.jpg
Ignicoccus hospitalis (and its symbiote Nanoarchaeum equitans )
Scientific classification
Domain:
Archaea
(unranked):
Karyota

Lake (1988) [1]
Domain & Regnum
Synonyms
  • proto-eukaryotic group
  • Karyotes

The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes (later classified as Thermoproteota, a group of archaea). [3] After his team at the University of California, Los Angeles discovered eocytes in 1984, [2] James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: prokaryotes, which include Bacteria and Archaea, and karyotes, that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria. [4]

Contents

Lake's hypothesis was based on an analysis of the structural components of ribosomes. It was largely ignored, being overshadowed by the three-domain system which relied on more precise genetic analysis. In 1990, Carl Woese and his colleagues proposed that cellular life consists of three domains – Eucarya, Bacteria, and Archaea – based on the ribosomal RNA sequences. The three-domain concept was widely accepted in genetics, and became the presumptive classification system for high-level taxonomy, and was promulgated in many textbooks. [5] [6]

Resurgence of archaea research after the 2000s, using advanced genetic techniques, and later discoveries of new groups of archaea revived the eocyte hypothesis; consequently, the two-domain system has found wider acceptance. [7] [8]

Description

In 1984, James A. Lake, Michael W. Clark, Eric Henderson, and Melanie Oakes of the University of California, Los Angeles described a new group of prokaryotic organisms designated as "a group of sulfur-dependent bacteria." Based on the structure and composition of their ribosomal subunits, they found that these organisms were different from other prokaryotes, bacteria and archaea, known at the time. They named them eocytes (for "dawn cells") and proposed a new biological kingdom Eocyta. According to this discovery, the tree of life is represented by four kingdoms, Archaebacteria, Eubacteria, Eukaryote and Eocyta. [2]

Following analyses of the rRNA sequences of the four groups, Lake concluded in 1988 that eukaryotes were closely related to eocytes such that the two groups constitute the same (monophyletic) group, meaning that eukaryotes originated from eocytes and not archaebacteria, as was generally assumed. [9] This was the establishment of the eocyte hypothesis. [3] In 1988, Lake proposed a systematic classification of all life forms into two taxonomic groups, [1] which he later mentioned as superkingdoms: [10]

  1. Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes)
  2. Parkaryotes (that consists of eubacteria and two groups of archaea known at the time, halobacteria and methanogens) [11]

Development and competition

Lake's classification was not widely recognised, but the eocyte hypothesis gained considerable attention after its introduction due to the interest in determining the origin of the eukaryotic cell. [12] [13] However, the concept faced a problem because it was not known that eocytes, the main organism group on which the hypothesis was based, were archaea. For example, studies in the late 1980s and early 1990s still treated eocytes as separate group from archaea. [12] [14] [15] As Lake also argued, the rival hypothesis was called archaebacterial tree (as introduced by Carl Woese of the University of Illinois in 1987 [16] ) or archaebacterial theory, which (supposedly) stated that eukaryotes originated from archaea, and not eocytes. [10] [17]

Due to such confusion, some studies appeared to invalidate the hypothesis. For example, Japanese scientists reported in 1990 their study on the elongation factors Tu(EF-Tu) and G(EF-G) from various organisms that showed that eukaryotes are most closely related to archaea (methanogen and halobacteria), and not eocytes. [15] Other studies also supported the eukaroyte-archaea relationship and rejected the eocyte hypotheses. [13] [18] [19] Ribosomal RNA sequencing in 1989 also opposed the eocyte tree as the origin of eukaryotes. [12]

Three-domain system

The most important blow to eocyte hypothesis and Lake's classification was the development of ribosomal RNA sequencing that became a reliable determinant in biological classification. [20] [21] Introduced in 1977 by Carl Woese and George E. Fox [22] in classification, the technique indicated that archaea (with only methanogens known at the time) and bacteria were distinct groups of organisms. Two kingdoms, Archaebacteria (archaea) and Eubacteria (for bacteria) were established. [22] Based on further studies, Woese, Otto Kandler and Mark Wheelis introduced the concept of "domain" in 1990 as the highest level of biological classification, and proposed the three-domain system consisting of Eucarya, Bacteria and Archaea. [23] With it they classified eocytes as archaea under the phylum Crenarchaeota [24] (which was reclassified as Thermoproteota in 2021 [25] ).

The classification gradually gained acceptance and was recognised as "arguably the best-developed and most widely-accepted scientific hypotheses [with the five-kingdom classification] regarding the evolutionary history of life." [26] It became a scientific concept and general taxonomy in textbooks. [5] [6] Although Lake continued to advocate his eocyte taxonomy and hypothesis instead of conceding that eocytes were archaea, [10] [27] the hypothesis was largely neglected [28] and support of it waned in favour of the three-domain system. [3]

Archaeal studies

In addition to a Thermoproteota origin of eukaryotes, some studies have suggested that eukaryotes may also have originated in the Nitrososphaerota (formerly Thaumarchaeota). [3] [29] [30] [31] [32] A superphylum — TACK — has been proposed that includes the Nitrososphaerota, Thermoproteota, and other groups of archaea, [31] so that this superphylum may be related to the origin of eukaryotes. It is seen that eukaryotes share a large number of proteins with members of the TACK superphylum and that these complex archaea may have had rudimentary phagocytosis abilities to engulf bacteria. [24]

As a result of metagenomic analysis of material found nearby hydrothermal vents, another superphylum — Asgard — has been named and proposed to be more closely related to the original eukaryote and a sister group to TACK more recently. Asgard consists of phyla Lokiarchaeota (found first), Heimdallarchaeota (possibly related closest to eukaryotes) and others. [33] [34]

Root of the eocyte tree

Schematic representation Eocyte hypothesis.png
Schematic representation

The eocyte tree root may be located in the RNA world; that is, the root organism may have been a ribocyte (also known as a ribocell). For cellular DNA and DNA handling, an "out of virus" scenario has been proposed: storing genetic information in DNA may have been an innovation performed by viruses and later handed over to ribocytes twice, once transforming them into bacteria and once transforming them into archaea. [35] [36]

Although archaeal viruses are not as well-studied as bacterial phages, it is thought that dsDNA viruses led to the incorporation of the viral genome into archaeal genomes. [37] The transduction of genetic material through a viral vector led to an increase in complexity in the pre-eukaryotic cells. [38] All these findings do not change the eocyte tree as given here in principle, but examine a higher resolution of it.

Arguments against

Due to the similarities found between eukaryotes and both archaea and bacteria, it is thought that a major source of the genetic variation is through horizontal gene transfer. [39] Horizontal gene transfer explains why archaeal sequences are found in bacteria and bacterial sequences are found in archaea. [39] This could explain why elongation factors found in archaea and eukaryotes are so similar, the data currently out is obscured as horizontal gene transfer, vertical gene transfer, or endosymbiosis and could be behind the gene sequence similarity. [40] The eocyte hypothesis also has troubles due to the endosymbiotic theory, with the archaea being able to phagocytize bacteria for the formation of membrane-bound organelles. [41] It is thought that these ancestral prokaryotes began to have ectosymbiotic relationships with other prokaryotes and gradually engulfed these symbiotes through cell membrane protrusions. [42]

Although more recent data provides evidence in favour of the relationship between eukaryotes and Thermoproteota through the analysis of elongation factors, earlier experimentation with elongation factors provided evidence against such a relationship. [15] Hasegawa et al. uses these elongation factors to show that eukaryotes and archaebacteria are more closely related than archaebacteria and eubacteria than is explained in this two-tree system. [15]

Competing hypothesis

A competing hypothesis is that prokaryotes evolved towards thriving in higher temperatures to evade viruses through the thermoreductive hypothesis, however this does not account for the arising of eukaryotes and only takes into consideration the prokaryotic origins. [43] However decrease in complexity from a more complex origin is the basis of reductive evolution where a commensal relationship occurs, while this reduction explained in the thermoreduction hypothesis uses a parasitic relationship with viruses to explain the movement of complex pre-eukaryotes to a more harsh environment; that being ocean floor hydrothermal vents. [44]

Revival

Molecular studies

With advancements in genomics, the eocyte hypothesis experienced a revival beginning in the mid-2000s. As more archaeal genomes were sequenced, numerous genes coding for eukaryotic traits have been discovered in various archaean phyla, seemingly providing support for the eocyte hypothesis. Proteomics based research has also found supporting data with the use of elongation factor 1-α (eEF-1), a common housekeeping protein, to compare structural homology between eukaryotic and archaean lineages. [45] Furthermore, other proteins have been sequenced through proteomics with homologous structures in heat shock proteins found in both eukaryotes and archaea. The structure of these heat shock proteins were identified through X-ray crystallography to find the three dimensional structure of the proteins. [10] These proteins however have differing purposes as the eukaryote heat shock protein is a part of the T-complex while the archaeal heat shock protein is a molecular chaperone. [10] This creates an issue with the sequence homology that has been seen between 70 kilodalton heat shock proteins in eukaryotes and Gram-negative bacteria. [40]

Ribosome protein sequencing and phylogenetic analyses in 2004 showed that eukaryotes emerged from archaea. [46] [47] Phylogenomic analysis in 2007 also pointed to the origin of eukaryotes specifically from the Thermoplasmatales. [48] The so-called "eukaryotic signature proteins" actin (cytoskeletal microfilament involved in cell motility), tubulin (component of the large cytoskeleton, microtubule) and the ubiquitin system (protein degradation and recycling) [7] [49] which are thought to be unique to eukaryotes were found in TACK (comprising the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) archaea but not in other archaea. These indicate that eukaryotes can be merged into archaea. [24]

Discovery of Asgards

Asgard, described as "eukaryote-like archaea", [50] were discovered in 2012. [51] [52] The first known Asgards called Lokiarchaeota contain more eukaryotic protein-genes than the TACK group that supported the merging of eukaryote–archaea grouping, meaning a single domain of Archaea. [53] [54] Phylogenomic studies indicated that Heimdallarchaeota, another group of Asgards, are the closest relatives of eukaryotes. [34] [55] [56] A new group of Asgard described in 2021 (named Wukongarchaeota) are also among the eukaryotic roots. [57] Another new Asgard reported in 2022, named Njordarchaeota, is related to the Heimdallarchaeota–Wukongarchaeota branch and is possibly the origin group for eukaryotes. [58]

The Asgards contain at least 80 genes for eukaryotic signature proteins. [59] In addition to actin, tubulin, ubiquitin and ESCRT proteins found in TACK archaea, Asgards contain functional genes for several other eukaryotic proteins such as profilins, [60] ubiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins), [61] membrane-trafficking systems (such as Sec23/24 and TRAPP domains), variety of small GTPases [62] (including Gtr/Rag family GTPase orthologues [63] ), and gelsolins. [64]

The two-domain system

As more archaea were later discovered and better genetic analysis were available, it was realised that the three-domain concept might not have represented the correct origin of eukaryotes. [65] [32] Ford Doolittle, then at the Dalhousie University, Canada, wrote in 2020:

"[The] three-domain tree wrongly represents evolutionary relationships, presenting a misleading view about how eukaryotes evolved from prokaryotes. The three-domain tree does recognize a specific archaeal–eukaryotic affinity, but it would have the latter arising independently, not from within, the former." [66]

This is because research since the early 2000s have revealed two important issues: eukaryotes originated within Archaea, and a new group of archaea called Asgards represent the root of eukaryotes. [67] [68] This led to the rebirth of the eocyte hypothesis and development of the two-domain system. [3]

Discoveries of eukaryotic signature proteins in TACK and Asgard archaea support the notion that eukaryotes evolved from archaea. Discoveries of more Asgards and better understanding of their nature indicate that they are the likely root of eukaryotes and are considered the strong "evidence of the Eocyte hypothesis." [67] Although these facts do not completely rule out the three-domain concept, [50] they generally strengthened the two-domain system. [7] [56] [57]

Related Research Articles

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

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

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

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

<span class="mw-page-title-main">Three-domain system</span> Hypothesis for classification of life

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

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

The Thermoproteota are prokaryotes that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones. Until recently all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113°C. These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells.

<span class="mw-page-title-main">Korarchaeota</span> Proposed phylum within the Archaea

The Korarchaeota is a proposed phylum within the Archaea. The name is derived from the Greek noun koros or kore, meaning young man or young woman, and the Greek adjective archaios which means ancient. They are also known as Xenarchaeota. The name is equivalent to Candidatus Korarchaeota, and they go by the name Xenarchaeota or Xenarchaea as well.

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

Euryarchaeota is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extreme concentrations of salt, and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase.

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

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

Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within a methanogenic archaeon or a bacterium. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome and eventually usurping its role. The hypothesis was first proposed by Philip Bell in 2001 and was further popularized with the discovery of large, complex DNA viruses that are capable of protein biosynthesis.

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

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

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

A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό 'before' and κάρυον 'nut, kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota.

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

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

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

The eukaryotes constitute the domain of Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, 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.

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

James A. Lake is an American evolutionary biologist and a Distinguished Professor of Molecular, Cell, and Developmental Biology and of Human Genetics at UCLA. Lake is best known for the New Animal Phylogeny and for the first three-dimensional structure of the ribosome. He has also made significant contributions to understanding genome evolution across all kingdoms of life, including discovering informational and operational genes, elucidating the complexity hypothesis for gene transfer, rooting the tree of life, and understanding the early transition from prokaryotic to eukaryotic life.

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

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

<span class="mw-page-title-main">Eukaryogenesis</span> Process of forming the first eukaryotic cell

Eukaryogenesis, the process which created the eukaryotic cell and lineage, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The process is widely agreed to have involved symbiogenesis, in which archaea and bacteria came together to create the first eukaryotic common ancestor (FECA). This cell had a new level of complexity and capability, with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex, a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. It evolved into a population of single-celled organisms that included the last eukaryotic common ancestor (LECA), gaining capabilities along the way, though the sequence of the steps involved has been disputed, and may not have started with symbiogenesis. In turn, the LECA gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms.

<span class="mw-page-title-main">TACK</span> Clade of Archaea

TACK is a group of archaea, its name an acronym for Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota, the first groups discovered. They are found in different environments ranging from acidophilic thermophiles to mesophiles and psychrophiles and with different types of metabolism, predominantly anaerobic and chemosynthetic. TACK is a clade that is sister to the Asgard branch that gave rise to the eukaryotes. It has been proposed that the TACK clade be classified as Crenarchaeota and that the traditional "Crenarchaeota" (Thermoproteota) be classified as a class called "Sulfolobia", along with the other phyla with class rank or order.

<span class="mw-page-title-main">Asgard (archaea)</span> Proposed superphylum of archaea

Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that contain eukaryotic signature proteins. It appears that the eukaryotes, the domain that contains the animals, plants, and fungi, emerged within the Asgard, in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over the three-domain system.

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

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

References

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