Lokiarchaeota

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"Lokiarchaeota"
Systematics
Classification : Creature
Domain : Archaea (Archaea)
Department : "Proteoarchaea"
Class : "Lokiarchaeota"
Scientific name
"Lokiarchaeota"
Spang et al. 2015

The Lokiarchaeota (German: Lokiarchaeen ) are a systematic group of microorganisms in the taxonomic rank of a tribe , which is assigned to the domain of the archaea . The establishment of the taxon in 2015 was based primarily on molecular genetic data.

Although the Lokiarchaeen are prokaryotes , they contain some genes that have so far only been found in animals , plants , fungi and other eukaryotes , so-called eukaryotic signature genes . The Lokiarchaeen are therefore also discussed as a kind of missing link between archaea and eukaryotes. However, further investigations are necessary to confirm the missing link hypothesis, for example the detection of a dynamic cytoskeleton under the microscope.

Top (1 m) of a 12 m high chimney of the hydrothermal spring Loki's Castle . On the left of the picture is the arm of a remote-controlled underwater vehicle that was used to take water samples in 2008 by the Center for Geobiology at the University of Bergen .

The organic material in which the special genetic signature of the Lokiarcheen has been identified comes from samples of marine sediments taken from a geothermal area in the Arctic deep sea between northwest Europe and Greenland. This geothermal was because of the bizarre shapes of vents his black smokers by its discoverers " Loki's Castle (" English Loki's Castle ) called. The name "Lokiarchaeota" also refers to the fact that the Lokiarchaeen can change their cell shape and that the Nordic god Loki , according to legend, was a shape changer .

Discovery and Description

"Loki's Castle" is a geothermal area in a volcanically active deep sea region, in which chimneys made of sulfidic minerals have formed over hot springs, so-called black smokers . It is located at a depth of around 2300 m in the transition region from the North Atlantic to the Arctic Ocean on the mid-ocean ridge between Greenland and Scandinavia (transition from the poppy ridge to the Knipowitsch ridge).

In 2010 sediment samples were taken there, the metagenomic analysis of which by teams from Bergen , Uppsala in Christa Scheper’s working group at the University of Vienna provided a wealth of clues to previously unknown archaea. This included Lokiarchaeum , which so far could not be grown in pure culture in the laboratory . Because of the low cell density (cells per gram of sediment), the determined Lokiarchaeum DNA sequence does not come from an isolated cell, but rather from the combination of gene fragments from several individuals. The genome found is 92% complete and 1.4-fold redundant . The fragments come from three species of a new taxon (see figure below).

The genome of Lokiarchaeum consists of 5381 protein coding genes together. Of these, 32% do not match known proteins, 26% are closely related to the proteins of known archaea and 29% are related to bacterial proteins. This composition speaks for the following:

  1. These are proteins from a new strain that is adding a new basal taxon to the domain of the archaea .
  2. A particularly intensive horizontal gene transfer from bacteria to archaea has taken place. (For comparison: with methanosarcines “only” a proportion of 5% genes of bacterial origin were found.).

A small but significant proportion of the genes (175 = 3.3%) of Lokiarchaeum closely resemble the genes of eukaryotic proteins. These genes, which are very unusual for prokaryotes , hardly come from contamination of the samples, as they were always flanked by prokaryotic gene sequences. As expected, no genes of eukaryotic origin could be detected in the metagenome of the sediment samples from the thermophilic biotope . Proteins that Lokiarchaeum have in common with eukaryotes are components of the cytoskeleton in the latter and are used to deform the cell membrane and shape. Apparently Lokiarchaeum shares this ability. Another common protein, namely actin , is essential for phagocytosis in eukaryotes , i.e. the ability of organisms to flow around particles and take them up into the cell. If it is confirmed that Lokiarchaeen are also capable of phagocytosis, that would explain well how the symbiosis of archaea and bacteria came about. Lokiarchaeen or close relatives could have incorporated bacteria and used them as symbionts, which then developed into mitochondria according to the generally accepted endosymbiont theory.

Internal and external taxonomy of the "Lokiarchaeota" and meaning in evolution

Position of the Lokiarchaeota and the root of the eukaryotes in the archaea family tree, simplified according to Spang et al. It is based on the evaluation of the genes of 36 proteins, which are typical and highly conservative in eukaryotes. Since the analysis of these genes only allows limited conclusions about the roots of the archaea, the upper part of the family tree has been simplified. The superscript numbers are the taxonomy numbers in the Universal Protein Resource (UniProt). Lokiarchaeota can be found e.g. B. under http://www.uniprot.org/taxonomy/1655434 [1]

One of the three partial genomes found (see adjacent figure) has a significantly lower GC content than the other two. This means that they have a different content of the DNA bases guanine and cytosine in their DNA . This difference can only result from a significant amount of different point mutations in the two branches of the Lokiarchaeota .

The comparative study of the genomes of Lokiarchaeum and those of known eukaryotes strongly suggests that these organisms share a common phylogenetic past and a common monophyletic pedigree.

The generally recognized three-domain model from Carl Woese divides all cellular organisms into archaea , bacteria and eukaryotes . Eukaryotes are all multicellular cells such as animals, fungi, plants and the protozoa. Together they are characterized by their large, highly developed cells , whose energy balance is entirely based on mitochondrial ATP synthases and in which the DNA is embedded in a nuclear membrane . Bacteria and archaea appear to be their ancestors, and fossil traces of archaea lipids have been found 3.8 billion year old . The evolution of the eukaryotes was probably only completed 1.6 to 2.1 billion years ago. Lokiarchaeum is apparently a missing link for this evolution from prokaryotic archaea . Its last common ancestor with the eukaryotes probably developed the genes about two billion years ago that were indispensable for the development of complex eukaryotic cell structures and therefore acted like a “starter kit”.

The Lokiarchaeota themselves are placed in the Proteoarchaeota department described by Celine Petitjean and colleagues in 2014 . Together with their sister groups " Thorarchaeota ", " Odinarchaeota " and " Heimdallarchaeota ", which were later found, they form the subgroup " Asgard " of the Proteoarchaeota. "Asgard" then appears as a sister group of "TACK". According to cladistic argumentation, the eukaryota (and thus humans) would then also belong to the Asgard group.

A summary of this discussion can be found in Traci Watson (2019).

Individual evidence

  1. ↑ a b c d e f g h i j Anja Spang, Jimmy H. Saw, Steffen L. Jørgensen, Katarzyna Zaremba-Niedzwiedzka, Joran Martijn, Anders E. Lind, Roel van Eijk, Christa Schleper, Lionel Guy, Thijs JG Ettema : Complex archaea that bridge the gap between prokaryotes and eukaryotes . In: Nature . 521, 2015, ISSN  0028-0836 , pp. 173-179. doi : 10.1038 / nature14447 . PMID 25945739 . PMC 4444528 (free full text).
  2. ↑ Rolf B. Pedersen, Hans Tore Rapp, Ingunn H. Thorseth, Marvin D. Lilley, Fernando JAS Barriga, Tamara Baumberger, Kristin Flesland, Rita Fonseca, Gretchen L. Früh-Green, Steffen L. Jorgensen: Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge . In: Nature Communications . 1, item no. 126, 2010. doi : 10.1038 / ncomms1124 .
  3. ↑ a b Christa Schleper, Department of Ecogenomics and System Biology at the University of Vienna (scientific contact): New complex archaea discovered. Nearest relatives of the eukaryotes. In: LABO Online , May 7, 2015. Accessed February 17, 2016.
  4. ↑ Steffen Leth Jorgensen, Bjarte Hannisdal, Anders Lanzén, Tamara Baumberger, Kristin Flesland, Rita Fonseca, Lise Øvreås, Ida H. Steen, Ingunn H. Thorseth, Rolf B. Pedersen, Christa Schleper: Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge . In: Proceedings of the National Academy of Sciences . tape 109 , no. 42 , October 16, 2012, ISSN  0027-8424 , p. E2846 – E2855 , doi : 10.1073 / pnas.1207574109 ( pnas.org ).
  5. ↑ Steffen Leth Jørgensen, Ingunn Hindenes Thorseth, Rolf Birger Pedersen, Tamara Baumberger, Christa Schleper: Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge . In: Extreme Microbiology . tape 4 , October 4, 2013, p. 299 , doi : 10.3389 / fmicb.2013.00299 ( frontiersin.org ).
  6. ^ A b Paul Rincon: Newly found microbe is close relative of complex life. May 6, 2015.
  7. ↑ Sofya K. Garushyants, Marat D. Kazanov, Mikhail S. Gelfand: Horizontal gene transfer and genome evolution in Methanosarcina . In: BMC Evolutionary Biology . 15, No. 1, 2015, pp. 1–14. doi : 10.1186 / s12862-015-0393-2 .
  8. ↑ a b Umesh Ghoshdastider, Shimin Jiang, David Popp, Robert C. Robinson: In search of the primordial actin filament . In: Proceedings of the National Academy of Sciences . tape 112 , no. 30 , July 28, 2015, ISSN  1091-6490 , p. 9150-9151 , doi : 10.1073 / pnas.1511568112 , PMID 26178194 .
  9. ↑ Amina Khan: Meet Loki, your closest-known prokaryote relative. In: Los Angeles Times. May 6, 2015.
  10. ^ Steven G. Ball, Debashish Bhattacharya, Andreas PM Weber: Pathogen to powerhouse . In: Science . 351, No. 6274, 2016, pp. 659-660. doi : 10.1126 / science.aad8864 .
  11. ^ T. Martin Embley, William Martin: Eukaryotic evolution, changes and challenges . In: Nature . tape 440 , no. 7084 , March 30, 2006, ISSN  1476-4687 , p. 623-630 , doi : 10.1038 / nature04546 , PMID 16572163 .
  12. ↑ JA Lake: Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences . In: Nature . tape 331 , no. 6152 , January 14, 1988, ISSN  0028-0836 , p. 184-186 , doi : 10.1038 / 331184a0 , PMID 3340165 .
  13. ↑ Lionel Guy, Thijs JG Ettema: The archaeal 'TACK' superphylum and the origin of eukaryotes . In: Trends in Microbiology . tape 19 , no. 12 , December 1, 2011, ISSN  1878-4380 , p. 580-587 , doi : 10.1016 / j.tim.2011.09.002 , PMID 22018741 .
  14. ↑ Minglei Wang, Liudmila S. Yafremava, Derek Caetano-Anolles, Jay E. Mittenthal, Gustavo Caetano-Anolles: Reductive evolution of architectural repertoire in proteomes and the birth of the tripartite world . In: Genome Research . tape 17 , no. 11 , November 1, 2007, ISSN  1088-9051 , p. 1572–1585 , doi : 10.1101 / gr.6454307 , PMID 17908824 .
  15. ^ Jürgen Hahn, Pat Haug: Traces of archaebacteria in ancient sediments . In: Systematic and Applied Microbiology . tape 7 , no. 2 , May 1, 1986, pp. 178-183 , doi : 10.1016 / S0723-2020 (86) 80002-9 ( sciencedirect.com ).
  16. ↑ AH Knoll, EJ Javaux, D. Hewitt, P. Cohen: Eukaryotic organisms in Proterozoic oceans . In: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences . tape 361 , no. 1470 , June 29, 2006, ISSN  0962-8436 , p. 1023-1038 , doi : 10.1098 / rstb.2006.1843 , PMID 16754612 .
  17. ^ Purificación López-García, David Moreira: Open Questions on the Origin of Eukaryotes . In: Trends in Ecology & Evolution . 30, No. 11, 2015, pp. 697-708. doi : 10.1016 / j.tree.2015.09.005 .
  18. ↑ Tom A. Williams, Peter G. Foster, Cymon J. Cox, T. Martin Embley: An archaeal origin of eukaryotes supports only two primary domains of life . In: Nature . 504, No. 7479, 2013, pp. 231-236. doi : 10.1038 / nature12779 .
  19. ^ Carl Zimmer: Under the Sea, a Missing Link in the Evolution of Complex Cells . In: The New York Times . May 6, 2015, ISSN  0362-4331 ( nytimes.com ).
  20. ↑ Petitjean, C., Deschamps, P., López-García, P., and Moreira, D .: Rooting the Domain archaea by phylogenomic analysis supports the foundation of the new kingdom proteoarchaeota. . In: Genome Biol. Evol. . 7, 2014, pp. 191-204. doi : 10.1093 / gbe / evu274 .
  21. ↑ K Zaremba-Niedzwiedzka et al at al: Asgard archaea illuminate the origin of eukaryotic cellular complexity . In: Nature . 541, 2017, pp. 353-358. doi : 10.1038 / nature21031 .
  22. ↑ Traci Watson: The trickster microbes that are shaking up the tree of life , in: Nature from May 14, 2019 (English), Trickser bacteria shake the family tree of life , in: Spektrum.de from June 20, 2019 (German) - the term 'bacteria' is not entirely correct; the microbes considered are archaea or (according to some researchers) at least proto- eukaryotes different from bacteria .