Lokiarchaeota

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Lokiarchaeota
Candidatus Prometheoarchaeum syntrophicum SEM.jpg
SEM image of Candidatus Prometheoarchaeum syntrophicum
Scientific classification
Domain:
Archaea
Kingdom:
"Proteoarchaeota"
Superphylum:
Asgard
Phylum:
"Lokiarchaeota"

Spang et al. 2015
Class:
"Lokiarchaeia"

corrig. Spang et al. 2015
Order
  • "Lokiarchaeales" Spang et al. 2015

Lokiarchaeota is a proposed phylum of the Archaea. [1] 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. [2] 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.

Lokiarchaeota 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 vent field known as Loki's Castle located at the bend between Mohns/Knipovich ridge in the Arctic Ocean. [3]

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 [4] [5] 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. [6] The result was a 92% complete, 1.4 fold-redundant composite genome named Lokiarchaeum. [3]

The metagenomic analysis determined the presence of an organism's genome in the sample. [3] However, the organism itself was not cultured until years later, with a Japanese group first reporting isolation and cultivation of a Lokiarchaeota strain in 2019. [7] Since this initial cultivation of Lokiarchaeota, members of the phylum have been reported in a diverse range of habitats. Advances in both long and short-read technologies for DNA sequencing have also aided in the recovery and identification of Lokiarchaeota from microbial samples. [2]

The Lokiarchaeota phylum was proposed based on phylogenetic analyses using a set of highly conserved protein-coding genes. [3] 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. [6] 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", [8] an analogy to the role of Lokiarchaeota in debates about the origin of eukaryotes. [3]

Description

Candidatus Prometheoarchaeum syntrophicum. (c) SEM of a dividing cell. Scale bar = 1 mm. (d) Cryo-EM of a single cell. Scale bar = 500 mm. White arrows indicate large membrane vesicles. Candidatus Prometheoarchaeum syntrophicum SEM Cryo.jpg
Candidatus Prometheoarchaeum syntrophicum. (c) SEM of a dividing cell. Scale bar = 1 μm. (d) Cryo-EM of a single cell. Scale bar = 500 μm. White arrows indicate large membrane vesicles.

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. These proteins included homologs of cytoskeleton proteins, GTPases, and the oligosaccharyltransferase (OST) protein complex. Homologues for components of the endosomal sorting complex required for transport and the ubiquitin protein modifier system were also identified in Lokiarchaeota genome analysis. [2] 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. [3]

In eukaryotes, the function of these shared proteins include cell membrane deformation, cell shape formation, and a dynamic protein cytoskeleton. [3] [9] [10] Eukaryotic protein functions found in Lokiarchaeota also include intracellular transport mechanisms. [11] It is inferred then that Lokiarchaeum may have some of these abilities. [3] Another shared protein, actin, is essential for phagocytosis in eukaryotes. [6] [9] 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. [3] The presence of actin proteins and intracellular transport mechanisms provides evidence for the common ancestry between ancient Lokiarchaeota and eukarya. [11]

Taxonomy

Evolutionary significance

A schematic evolutionary tree of the archaea including Lokiarchaeota and the root of eukaryotes A schematic evolutionary tree of the archaea 2015 final.svg
A schematic evolutionary tree of the archaea including Lokiarchaeota and the root of eukaryotes

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, [14] supporting an archaeal host or eocyte-like scenarios for the emergence of the eukaryotes. [15] [16] [17] 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. [3]

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, [18] as fossil strata bearing the chemical signature of archaeal lipids have been dated back to 3.8 billion years ago. [19] The eukaryotes include all complex cells and almost all multicellular organisms. They are thought to have evolved between 1.6 and 2.1 billion years ago. [20] 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. [21] Lokiarchaeota and the eukaryotes probably share a common ancestor, and if so, diverged roughly two billion years ago. Evidence for common ancestry, rather than an evolutionary shift from Lokiarchaeota to eukaryotes, is found in analysis of fold superfamilies (FSFs). Fold super families are evolutionarily defined domains of protein structure. It is estimated that there are around 2500 total FSFs found in nature. [11] Utilization of Venn diagrams allowed researchers to depict distributions of FSFs of those that were shared by Archaea and Eukarya, as well as those unique to their respective kingdoms. The addition of Lokiarchaeum into the Venn groups created from an initial genomic census only added 10 FSFs to Archaea. The addition of Lokiarchaeum also only contributed to a decrease of two FSFs previously unique to Eukarya. There were still 284 FSFs found exclusively in Eukarya. Lokiarchaeota’s limited impact in changing the Venn distribution of FSFs demonstrates the lack of genes that could be traced to a common ancestor with Eukaryotes. Rather, Eukaryotic genes present in bacterial and archaeal organisms are hypothesized to be from horizontal transfer from an early ancestor of modern eukaryotes. [11] 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. [6]

In 2020, a Japanese research group reported culturing a strain of Lokiarchaeota in the laboratory. [22] [23] [7] This strain, currently named Candidatus Prometheoarchaeum syntrophicum strain MK-D1, was observed in syntrophic association with two hydrogen-consuming microbes: a sulfate-reducing bacteria of the genus Halodesulfovibrio and a methanogen of the genus Methanogenium . The MK-D1 organism produces hydrogen as a metabolic byproduct, which is then consumed by the symbiotic syntrophs. MK-D1 also seems to organize its external membrane into complex structures using genes shared with eukaryotes. While association with alphaproteobacteria (from which mitochondria are thought to descend) was not observed, these features suggest that MK-D1 and its syntrophs may represent an extant example of archaea-bacteria symbiosis similar to that which gave rise to eukaryotes.

In 2022, the second cultured example of Lokiarchaeota was reported and the strain was named Candidatus Lokiarchaeum ossiferum. [24]

Physiological traits

Lokiarachaeota is known to have a tetrahydromethanopterin-dependent Wood-Ljundahl pathway. This pathway contains a series of biochemical reactions aiding in inorganic carbon utilization. In Lokiarchaeota, the WLP is thought to be acetogenic, due to lacking the gene methyl-CoM reductase necessary for methanogenesis. [2]

Analysis of Lokiarchaeon genes also showed the expression of protein-encoding open reading frames (ORFs) involving the metabolism of sugars and proteins. However, these metabolic activities vary between subgroups of Lokiarchaeota. While Lokiarchaeota subgroups have similar genetic information, differences in metabolic abilities explain their respective ecological niches. [25]

Two major subgroups of the Lokiarachaeota phylum are Loki-2 and Loki-3. Incubations of these two subgroups from Helgoland mud sediments were analyzed through RNA and DNA stable isotope probing to understand their respective carbon metabolisms. [25] Loki-3 were found to be active in both organic carbon utilization and the degradation of aromatic compounds. The Loki-3 subgroup was not found to utilize proteins or short chain fatty acids, even though genes for amino acid degradation were present in both subgroups. Loki-2 was found to utilize protein, as seen through activity in when proteins were provided in Loki-2 incubations. Due to the greater carbon utilization pathways of Loki-3, the subgroup is found in a more diverse range of marine sediments than Loki-2. [25]

See also

Related Research Articles

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

The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. 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 a clade of Archaea.

<i>Nanoarchaeum equitans</i> Species of archaeon

Nanoarchaeum equitans is a species of marine archaea that was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. It has been proposed as the first species in a new phylum, and is the only species within the genus Nanoarchaeum. Strains of this microbe were also found on the Sub-polar Mid Oceanic Ridge, and in the Obsidian Pool in Yellowstone National Park. Since it grows in temperatures approaching boiling, at about 80 °C (176 °F), it is considered to be a thermophile. It grows best in environments with a pH of 6, and a salinity concentration of 2%. Nanoarchaeum appears to be an obligate symbiont on the archaeon Ignicoccus; it must be in contact with the host organism to survive. Nanoarchaeum equitans cannot synthesize lipids but obtains them from its host. Its cells are only 400 nm in diameter, making it the smallest known living organism, and the smallest known archaeon.

<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.

The hydrogen hypothesis is a model proposed by William F. Martin and Miklós Müller in 1998 that describes a possible way in which the mitochondrion arose as an endosymbiont within a prokaryotic host in the archaea, giving rise to a symbiotic association of two cells from which the first eukaryotic cell could have arisen (symbiogenesis).

<span class="mw-page-title-main">Last universal common ancestor</span> Most recent common ancestor of all current life on Earth

The last universal common ancestor (LUCA) is the hypothesized common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya originated. It is suggested to have been a "cellular organism that had a lipid bilayer and used DNA, RNA, and protein". The LUCA has also been defined as "a hypothetical organism ancestral to all three domains". The LUCA is the point or stage at which the three domains of life diverged from preexisting forms of life. The nature of this point or stage of divergence remains a topic of research.

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">Loki's Castle</span>

Loki's Castle is a field of five active hydrothermal vents in the mid-Atlantic Ocean, located at 73 degrees north on the Mid-Atlantic Ridge between Iceland and Svalbard at a depth of 2,352 metres (7,717 ft). They were the most northerly black smoker vents when they were discovered in mid-July 2008.

<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 prokaryotic. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

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

The Nitrososphaerota are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.

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

The eukaryotes constitute the domain of Eukarya or Eukaryota, 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.

<span class="mw-page-title-main">Eocyte hypothesis</span> Hypothesis in evolutionary biology

The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes. After his team at the University of California, Los Angeles discovered eocytes in 1984, 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.

The "Aigarchaeota" are a proposed archaeal phylum of which the main representative is Caldiarchaeum subterraneum. It is not yet clear if this represents a new phylum or a Nitrososphaerota order, since the genome of Caldiarchaeum subterraneum encodes several Nitrososphaerota-like features. The name "Aigarchaeota" comes from the Greek αυγή, avgí, meaning "dawn" or "aurora", for the intermediate features of hyperthermophilic and mesophilic life during the evolution of its lineage.

<span class="mw-page-title-main">Proteoarchaeota</span> Proposed kingdom of archaea

"Proteoarchaeota" are a proposed archaeal kingdom thought to be closely related and possibly ancestral to the Eukaryotes.

<span class="mw-page-title-main">DPANN</span> A superphylum of Archaea grouping taxa that display various environmental and metabolic features

DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.

"Candidatus Thorarchaeota", or simply Thorarchaeota, is a phylum within the superphylum Asgard archaea. The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes. Since there is such a close relation between the two different domains, it provides further evidence to the two-domain tree of life theory which states that eukaryotes branched from the archaeal domain. Asgard archaea are single cell marine microbes that contain branch like appendages and have genes that are similar to eukarya. The asgard archaea superphylum is composed of Thorarchaeota, Lokiarchaeota, Odinarchaeota, and Heimdallarchaeota. Thorarchaeota were first identified from the sulfate-methane transition zone in tidewater sediments. Thorarcheota are widely distributed in marine and freshwater sediments.

<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">Marine prokaryotes</span> Marine bacteria and marine archaea

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

<span class="mw-page-title-main">Archaeal virus</span> Type of virus that infects the domain of unicellular, prokaryotic organisms or Archaea

An archaeal virus is a virus that infects and replicates in archaea, a domain of unicellular, prokaryotic organisms. Archaeal viruses, like their hosts, are found worldwide, including in extreme environments inhospitable to most life such as acidic hot springs, highly saline bodies of water, and at the bottom of the ocean. They have been also found in the human body. The first known archaeal virus was described in 1974 and since then, a large diversity of archaeal viruses have been discovered, many possessing unique characteristics not found in other viruses. Little is known about their biological processes, such as how they replicate, but they are believed to have many independent origins, some of which likely predate the last archaeal common ancestor (LACA).

Christa Schleper is a German microbiologist known for her work on the evolution and ecology of Archaea. Schleper is Head of the Department of Functional and Evolutionary Biology at the University of Vienna in Austria.

<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 domains, Bacteria and Archaea. It emerged from development of knowledge of archaea diversity and challenges to the widely accepted three-domain system that classifies 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, thereby making eukaryotes members of the domain Archaea.

References

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