Asgard (Archaea)

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Asgard
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Archaea
Kingdom: Proteoarchaeota
Superphylum: Asgard
Katarzyna Zaremba-Niedzwiedzka  [ Wikidata ], et al. 2017
Phyla

see text

Global distribution of metagenomic-assembled sequences of Asgard archaea.png
Synonyms
  • "Asgardarchaeota" Violette Da Cunha et al. 2017
  • "Asgardaeota" Whitman 2018
  • "Eukaryomorpha" Fournier & Poole 2018 [1]
  • Promethearchaeati Imachi et al. 2024
  • Promethearchaeota Imachi et al. 2024

Asgard or Asgardarchaeota [2] is a proposed superphylum belonging to the domain Archaea that contain eukaryotic signature proteins. [3] It appears that the eukaryotes, the domain that contains the animals, plants, and fungi, emerged within the Asgard, [4] in a branch containing the Heimdallarchaeota. [5] This supports the two-domain system of classification over the three-domain system. [6] [7]

Contents

After including the kingdom category into ICNP, the only validly published name of this group is kingdom Promethearchaeati, containing only one phylum Promethearchaeota. All formerly proposed "phyla" would be de-ranked to classes in this framework. [8]

Discovery and nomenclature

In the summer of 2010, sediments were analysed from a gravity core taken in the rift valley on the Knipovich ridge in the Arctic Ocean, near the Loki's Castle hydrothermal vent site. Specific sediment horizons previously shown to contain high abundances of novel archaeal lineages were subjected to metagenomic analysis. [9] [10] In 2015, an Uppsala University-led team proposed the Lokiarchaeota phylum based on phylogenetic analyses using a set of highly conserved protein-coding genes. [11] The group was named for the shape-shifting Norse god Loki, in an allusion to the hydrothermal vent complex from which the first genome sample originated. [12] The Loki of mythology has been described as "a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies", [13] analogous to the role of Lokiarchaeota in the debates about the origin of eukaryotes. [11] [14]

In 2016, a University of Texas-led team discovered Thorarchaeota from samples taken from the White Oak River in North Carolina, named in reference to Thor, another Norse god. [15] Samples from Loki's Castle, Yellowstone National Park, Aarhus Bay, an aquifer near the Colorado River, New Zealand's Radiata Pool, hydrothermal vents near Taketomi Island, Japan, and the White Oak River estuary in the United States contained Odinarchaeota and Heimdallarchaeota; [3] following the Norse deity naming convention, these groups were named for Odin and Heimdall respectively. Researchers therefore named the superphylum containing these microbes "Asgard", after the home of the gods in Norse mythology. [3] Two Lokiarchaeota specimens have been cultured, enabling a detailed insight into their morphology. [16]

Description

Proteins

Asgard members encode many eukaryotic signature proteins, including novel GTPases, membrane-remodelling proteins like ESCRT and SNF7, a ubiquitin modifier system, and N-glycosylation pathway homologs. [3]

Asgard archaeons have a regulated actin cytoskeleton, and the profilins and gelsolins they use can interact with eukaryotic actins. [17] [18] In addition, Asgard archaea tubulin from hydrothermal-living Odinarchaeota (OdinTubulin) was identified as a genuine tubulin. OdinTubulin forms protomers and protofilaments most similar to eukaryotic microtubules, yet assembles into ring systems more similar to FtsZ, indicating that OdinTubulin may represent an evolution intermediate between FtsZ and microtubule-forming tubulins. [19] They also seem to form vesicles under cryogenic electron microscopy. Some may have a PKD domain S-layer. [20] They also share the three-way ES39 expansion in LSU rRNA with eukaryotes. [21] Gene clusters or operons encoding ribosomal proteins are often less conserved in their organization in the Asgard group than in other Archaea, suggesting that the order of ribosomal protein coding genes may follow the phylogeny. [22]

Metabolism

Asgard archaea are generally obligate anaerobes, though Kariarchaeota, Gerdarchaeota and Hodarchaeota may be facultative aerobes. [24] They have a Wood–Ljungdahl pathway and perform glycolysis. Members can be autotrophs, heterotrophs, or phototrophs using heliorhodopsin. [23] One member, CandidatusPrometheoarchaeum syntrophicum, is syntrophic with a sulfur-reducing proteobacteria and a methanogenic archaea. [20]

The RuBisCO they have is not carbon-fixing, but likely used for nucleoside salvaging. [23]

Ecology

Asgard are widely distributed around the world, both geographically and by habitat. Many of the known clades are restricted to sediments, whereas Lokiarchaeota, Thorarchaeota and another clade occupy many different habitats. Salinity and depth are important ecological drivers for most Asgard archaea. Other habitats include the bodies of animals, the rhizosphere of plants, non-saline sediments and soils, the sea surface, and freshwater. In addition, Asgard are associated with several other microorganisms. [25]

Eukaryote-like features in subdivisions

The phylum Heimdallarchaeota was found in 2017 to have N-terminal core histone tails, a feature previously thought to be exclusively eukaryotic. Two other archaeal phyla, both outside of Asgard, were found to also have tails in 2018. [26]

In January 2020, scientists found CandidatusPrometheoarchaeum syntrophicum, a member of the Lokiarcheota, engaging in cross-feeding with two bacterial species. Drawing an analogy to symbiogenesis, they consider this relationship a possible link between the simple prokaryotic microorganisms and the complex eukaryotic microorganisms occurring approximately two billion years ago. [27] [20]

Phylogeny

The phylogenetic relationships of the Asgard archaea have been studied by several teams in the 21st century. [5] [4] [28] [24] Varying results have been obtained, for instance using 53 marker proteins from the Genome Taxonomy Database. [29] [30] [31] In 2023, Eme, Tamarit, Caceres and colleagues reported that the Eukaryota are deep within Asgard, as sister of Hodarchaeales within the Heimdallarchaeota. [32]


Eme et al. 2023 [32] 09-RS220 (24 April 2024) [29] [30] [31]
Proteoarchaeota
Thermoproteati

Thermoproteota (TACK)

Promethearchaeati:

"Thorarchaeia" (MBG-B)

"Njordarchaeia"

"Odinarchaeia"

"Jordarchaeia"
"Jordarchaeales"

"Freyrarchaeaceae"

"Jordarchaeaceae"

"Baldrarchaeia"

"Hermodarchaeia"

Promethearchaeia

"Helarchaeales"

Promethearchaeales

"Sigynarchaeaceae"

Promethearchaeaceae
["Lokiarchaeaceae"]

"Sifarchaeia"

"Sifarchaeales"

"Borrarchaeales"

"Wukongarchaeia"

"Heimdallarchaeia"

"Hodarchaeales"

"Gerdarchaeales" (JABLTI01)

"Kariarchaeales"

"Heimdallarchaeales"

Promethearchaeota

Taxonomy

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. Symbiogenesis 2 mergers.svg
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.

In the depicted scenario, the Eukaryota are deep in the tree of Asgard. A favored scenario is syntrophy, where one organism depends on the feeding of the other. An α-proteobacterium was incorporated to become the mitochondrion. [34] In culture, extant Asgard archaea form various syntrophic dependencies. [35] Gregory Fournier and Anthony Poole have proposed that Asgard is part of "the Eukaryote tree", forming a superphylum they call "Eukaryomorpha" defined by "shared derived characters" (eukaryote signature proteins). [36]

The taxonomy is uncertain and the phylum names are therefore somewhat speculative. The list of phyla is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [37] and National Center for Biotechnology Information (NCBI). [38]

Genomic elements

Viruses

Several family-level groups of viruses associated with Asgard archaea have been discovered using metagenomics. [39] [40] [41] The viruses were assigned to Lokiarchaeia, Thorarchaeia, Odinarchaeia and Helarchaeia hosts using CRISPR spacer matching to the corresponding protospacers within the viral genomes. Two groups of viruses (called 'verdandiviruses') are related to archaeal and bacterial viruses of the class Caudoviricetes , i.e., viruses with icosahedral capsids and helical tails; [39] [41] two other distinct groups (called 'skuldviruses') are distantly related to tailless archaeal and bacterial viruses with icosahedral capsids of the realm Varidnaviria ; [39] [40] and the third group of viruses (called wyrdviruses) is related to archaea-specific viruses with lemon-shaped virus particles (family Halspiviridae ). [39] [40] The viruses have been identified in deep-sea sediments [39] [41] and a terrestrial hot spring of the Yellowstone National Park. [40] All these viruses display very low sequence similarity to other known viruses but are generally related to the previously described prokaryotic viruses, [42] with no meaningful affinity to viruses of eukaryotes. [43] [39]

Mobile genetic elements

In addition to viruses, several groups of cryptic mobile genetic elements have been discovered through CRISPR spacer matching to be associated with Asgard archaea of the Lokiarchaeia, Thorarchaeia and Heimdallarchaeota lineages. [39] [44] These mobile elements do not encode recognizable viral hallmark proteins and could represent either novel types of viruses or plasmids.

See also

Related Research Articles

<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">Tubulin</span> Superfamily of proteins that make up microtubules

Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton. It was discovered and named by Hideo Mōri in 1968. Microtubules function in many essential cellular processes, including mitosis. Tubulin-binding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division.

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).

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">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 (pró), meaning 'before', and κάρυον (káruon), meaning 'nut' or 'kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. However 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 organisms

Archaea is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic, as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" in English still generally refers specifically to prokaryotic members of Archaea. 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 Eukaryota or 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.

The archaellum is a unique structure on the cell surface of many archaea that allows for swimming motility. The archaellum consists of a rigid helical filament that is attached to the cell membrane by a molecular motor. This molecular motor – composed of cytosolic, membrane, and pseudo-periplasmic proteins – is responsible for the assembly of the filament and, once assembled, for its rotation. The rotation of the filament propels archaeal cells in liquid medium, in a manner similar to the propeller of a boat. The bacterial analog of the archaellum is the flagellum, which is also responsible for their swimming motility and can also be compared to a rotating corkscrew. Although the movement of archaella and flagella is sometimes described as "whip-like", this is incorrect, as only cilia from Eukaryotes move in this manner. Indeed, even "flagellum" is a misnomer, as bacterial flagella also work as propeller-like structures.

<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.

<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">Proteoarchaeota</span> Proposed kingdom of archaea

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

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

Parvarchaeota is a phylum of archaea belonging to the DPANN archaea. They have been discovered in acid mine drainage waters and later in marine sediments. The cells of these organisms are extremely small consistent with small genomes. Metagenomic techniques allow obtaining genomic sequences from non-cultured organisms, which were applied to determine this phylum.

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

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<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 an archeon and a bacterium 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.

"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">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. After including the kingdom category into ICNP, the only validly published name of this group is kingdom Thermoproteati.

<span class="mw-page-title-main">Ubiquitin-like protein</span> Family of small proteins

Ubiquitin-like proteins (UBLs) are a family of small proteins involved in post-translational modification of other proteins in a cell, usually with a regulatory function. The UBL protein family derives its name from the first member of the class to be discovered, ubiquitin (Ub), best known for its role in regulating protein degradation through covalent modification of other proteins. Following the discovery of ubiquitin, many additional evolutionarily related members of the group were described, involving parallel regulatory processes and similar chemistry. UBLs are involved in a widely varying array of cellular functions including autophagy, protein trafficking, inflammation and immune responses, transcription, DNA repair, RNA splicing, and cellular differentiation.

<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">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 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.

Heimdallarchaeota is a group of archaea that in turn forms a distinct group within the superphylum Asgard. Named after the mythical Norse god, Heimdall, one of the sons of Odin, it consist of several archaea that are considered as the closest relatives of eukaryotic organism. The first specimens were discovered from the marine sediments at Loki's Castle and Bay of Aarhus, and some other species from Auka hydrothermal vent field in the Pacific Ocean. Proposed as a phylum, it consists of a class Heimdallarchaeia, that contains at least three orders and three genera. Discovered by team of microbiologists at the Uppsala University, Sweden, led by Thijs Johannes Gerardus Ettema, and reported in 2017, Heimdallarchaeota is the group to which eukaryotes, or more specifically, from where the common ancestor of all eukaryotes emerged.

References

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