Lokiarchaeota

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Lokiarchaeota
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

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 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

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

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

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

  • Order "Lokiarchaeales" Spang et al. 2015[12][13]
    • Family "Lokiarchaeaceae" Vanwonterghem et al. 2016 (MBGB, DSAG)
      • Genus "Candidatus
        Lokiarchaeum
        " corrig. Spang et al. 2015
        • "Ca. L. ossiferum" Rodrigues-Oliveira et al. 2023
    • Family "Prometheoarchaeaceae" Pallen, Rodriguez-R & Alikhan 2022 (MK-D1)
      • Genus "Candidatus Harpocratesius" Wu et al. 2022
        • "Ca. H. repetitus" Wu et al. 2022
      • Genus "Candidatus Promethearchaeum" corrig. Imachi, Nobu & Takai 2020
        • "Ca. P. syntrophicum" corrig. Imachi, Nobu & Takai 2020

Evolutionary significance

A schematic evolutionary tree of the archaea including Lokiarchaeota and the root of eukaryotes[3]

A comparative analysis of the Lokiarchaeum genome against known genomes resulted in a

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]

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.

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

References

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    S2CID 213982145. {{cite journal}}: Cite journal requires |journal= (help
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  6. ^ a b c d Rincon, Paul (May 6, 2015). "Newly found microbe is close relative of complex life". BBC. Retrieved May 9, 2015.
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  8. doi:10.1086/463618
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  10. LA Times
    . Retrieved May 9, 2015.
  11. ^
    PMID 26112912
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  12. ^ J.P. Euzéby. "Family: Lokiarchaeota, not assigned to family". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2023-06-20.
  13. ^ Sayers; et al. "Candidatus Lokiarchaeota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2023-06-20.
  14. ^ Maximillan, Ludwig (27 December 2019). "Evolution: A revelatory relationship". Phys.org. Retrieved 28 December 2019.
  15. S2CID 4396543
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  19. doi:10.1016/S0723-2020(86)80002-9
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  20. PMID 16754612
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  21. New York Times
    . Retrieved 8 May 2015.
  22. ^ Timmer, John (2019-08-07). "We've finally gotten a look at the microbe that might have been our ancestor". Ars Technica. Retrieved 2019-08-08.
  23. ^ Zimmer, Carl (2020-01-15). "This Strange Microbe May Mark One of Life's Great Leaps". The New York Times. Retrieved 2020-01-15.
  24. PMID 36544020
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  25. ^
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External links
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