Eocyte hypothesis

Karyota
Ignicoccus hospitalis (and its symbiote Nanoarchaeum equitans)
Scientific classification
Domain:	Archaea
(unranked):	Karyota Lake et al. 1988[1]
Domain & Regnum
Domain - Eukaryota Regnum - Eocyta Lake et al. 1984 unranked - TACK Phylum - Crenarchaeota Phylum - (Thaumarchaeota) unranked - Asgard(archaeota) Phylum - (Lokiarchaeota) Phylum - (Heimdallarchaeota)
Synonyms
proto-eukaryotic group Karyotes

The eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota (formerly known as eocytes), a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major phylum of archaea, the Euryarchaeota.^[2][3]

Schematic representation

Introduction

The eocyte hypothesis gained considerable attention after its introduction due to the interest in determining the origin of the eukaryotic cell. This hypothesis has primarily been in contrast with the three-domain system introduced by Carl Woese in 1977. Additional evidence supporting the eocyte hypothesis was published in the 1980s, but despite fairly unequivocal evidence, support waned in favor of the three-domain system.^[1][2]

Genomic advancements

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.^[4] 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.^[5] 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.^[5] This creates an issue with the sequence homology that has been seen between 70 kilodalton heat shock proteins in eukaryotes and gram negative bacteria.^[6]

Studies

In addition to a Crenarchaeal origin of eukaryotes, some studies have suggested that eukaryotes may also have originated in the Thaumarchaeota.^{[2][7][8][9][10]}

A superphylum — TACK — has been proposed that includes the Thaumarchaeota, Crenarchaeota, and other groups of archaea,^[11] 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.^[12]

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.^[13][14]

Root of the eocyte tree

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.^[15][16]

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.^[17] The transduction of genetic material through a viral vector led to an increase in complexity in the pre-eukaryotic cells.^[18] 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.^[19] Horizontal gene transfer explains why archaeal sequences are found in bacteria and bacterial sequences are found in archaea.^[19] 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.^[6] 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.^[20] It is thought that these ancestral prokaryotes began to have ectosymbiotic relationships with other prokaryotes and gradually engulfed these symbiotes through cell membrane protrusions.^[21]

Although more recent data provides evidence in favour of the relationship between eukaryotes and Crenarchaeota through the analysis of elongation factors, earlier experimentation with elongation factors provided evidence against such a relationship.^[22] 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 2 tree system.^[22]

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.^[23] 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.^[24]

References