Lokiarchaeota

Lokiarchaeota
Scientific classification
Domain:	Archaea
Kingdom:	"Proteoarchaeota" or incertae sedis
Phylum:	"Lokiarchaeota" Spang et al. 2015
Genus
"Candidatus Lokiarchaeum" Spang et al. 2015

Lokiarchaeota is a proposed phylum of the Archaea. 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.

Lokiarcheota was introduced in 2015 after the identification of a candidate genome in a metagenomic analysis of a mid-oceanic sediment sample. This analysis suggests the existence of a genus of unicellular life dubbed Lokiarchaeum. The sample was taken near a hydrothermal vent at a site known as Loki's Castle on Gakkel Ridge in the Arctic Ocean.

Discovery

Sediments from a gravity core taken in 2010 in the rift valley on the Knipovich ridge in the Arctic Ocean, near the so-called Loki's Castle hydrothermal vent site, were analysed. Specific sediment horizons, previously shown to contain high abundances of novel archaeal lineages were subjected to metagenomic analysis. Due to the low density of cells in the sediment, the resulting genetic sequence does not come from an isolated cell, as would be the case in conventional analysis, but is rather a combination of genetic fragments. The result was a 92% complete, 1.4 fold-redundant composite genome named Lokiarchaeum.

The metagenomic analysis determined the presence of an organism's genome in the sample. However, the organism itself has not been cultured.

The Lokiarchaeota phylum was proposed based on phylogenetic analyses using a set of highly conserved protein-coding genes. Through a reference to the hydrothermal vent complex from which the first genome sample originated, the name refers to Loki, the Norse shape-shifting god. The Loki of literature has been described as "a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies", in analogy to the ongoing debates on the origin of eukaryotes.

Description

The Lokiarchaeum composite genome consists of 5,381 protein coding genes. Of these, roughly 32% do not correspond to any known protein, 26% closely resemble archaeal proteins, and 29% correspond to bacterial proteins. This situation is consistent with: (i) proteins from a novel phylum (with few close relatives, or none) being difficult to assign to their correct domain; and (ii) existing research that suggests there has been significant inter-domain gene transfer between bacteria and Archaea.

A small, but significant portion of the proteins (175, 3.3%) that the recovered genes code for are very similar to eukaryotic proteins. Sample contamination is an unlikely explanation for the unusual proteins because the recovered genes were always flanked by prokaryotic genes and no genes of known eukaryotic origin were detected in the metagenome from which the composite genome was extracted. Further, previous phylogenetic analysis suggested the genes in question had their origin at the base of the eukaryotic clades.

In eukaryotes, the function of these shared proteins include cell membrane deformation, cell shape formation, and a dynamic protein cytoskeleton. It is inferred then that Lokiarchaeum may have some of these abilities. Another shared protein, actin, is essential for phagocytosis in eukaryotes. Phagocytosis is the ability to engulf and consume another particle; such ability would facilitate the endosymbiotic origin of mitochondria and chloroplasts, which is a key difference between prokaryotes and eukaryotes.

Evolutionary significance

A comparative analysis of the Lokiarchaeum genome against known genomes resulted in a phylogenetic tree that showed a monophyletic group composed of the Lokiarchaeota and the eukaryotes, supporting an archaeal host or eocyte-like scenarios for the emergence of the eukaryotes. The repertoire of membrane-related functions of Lokiarchaeum suggests that the common ancestor to the eukaryotes might be an intermediate step between the prokaryotic cells, devoid of subcellular structures, and the eukaryotic cells, which harbor many organelles.

Carl Woese's three-domain system classifies cellular life into three domains: archaea, bacteria, and eukaryotes; the last being characterised by large, highly evolved cells, containing mitochondria, which help the cells produce ATP (adenosine triphosphate, the energy currency of the cell), and a membrane-bound nucleus containing nucleic acids. Protozoa and all multicellular organisms such as animals, fungi, and plants are eukaryotes.

The bacteria and archaea are thought to be the most ancient of lineages, as fossil strata bearing the chemical signature of archaeal lipids have been dated back to 3.8 billion years ago. The eukaryotes include all complex cells and almost all multicellular organisms. They are considered to have evolved between 1.6 to 2.1 billion years ago. While the evolution of eukaryotes is considered to be an event of great evolutionary significance, no intermediate forms or "missing links" had been discovered previously. In this context, the discovery of Lokiarchaeum, with some but not all of the characteristics of eukaryotes, provides evidence on the transition from archaea to eukaryotes.

Lokiarchaeota and the eukaryotes probably share a common ancestor, and if so, diverged roughly two billion years ago. This putative ancestor possessed crucial "starter" genes that enabled increased cellular complexity. This common ancestor, or a relative, eventually led to the evolution of eukaryotes.