Lokiarchaeota: Missing link for complex cells?


History has given us many puzzles to solve in the field of evolution. According to a recent study, scientists at the Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden, identified a new class of Archaea, a microorganism that is made up of simple cells like bacteria, called “Lokiarchaeota”, which was noted as a possible missing link between bacteria and their more complex cousins, eukaryotes.

In fact, the evolutionary relationship between archaea and eukaryotes remains unclear. The Archaea constitute a domain of single-celled microorganisms. Now, the new class of organism was found in a hydrothermal vent system, a key site in emerging microorganism biology and study. This new archaeal phylum represents the closest known relatives of eukaryotes, the group encompassing all organisms that have nucleated cells. Interestingly this discovery holds promise for a better understanding of eukaryotic origins in coming years.

Phylogenetic tree of life
Phylogenetic tree of life

Thijs Ettema and his colleagues analyzed the genome of Loki, and found that it shares some genes with eukaryotes that other Archaea do not, which suggests it is a missing link for complex cells and shares characteristics between organisms. Loki is a prokaryotic microbes consisting eukaryote-like genes

Previously it was believed that both eukaryotes and archaea have been considered ‘sister groups’ based on their resemblance in genes and metabolic pathways. The present study with sequencing analysis revealed that these microbes belonged to one of the most abundant groups of marine archaea, and none of which have been cultured or sequenced. In addition, using deep metagenomics techniques, Ettema and his colleagues then assembled a 92 % complete, 5.1 mega base pair composite genome sequence for Lokiarchaea. Approximately 175 predicted proteins in these microbes were more similar to eukaryotic proteins that are involved in phagocytosis, cell shape formation, and membrane remodeling. Moreover, phylogenetic analysis revealed that eukaryotes clustered within this archaeal group rather than as a related branch on the tree.

Lokiarchaea have many other archaeal features, and the sediment sample appeared free of 18s rRNA sequences (a characteristic of eukaryotes). They also found that the Lokiarchaea genome contains 5 actin homologs that are more similar to eukaryotic actins than to archaeal actin-like proteins. Nearly 70 homologs of Ras-family small GTPases were also found, accounting for approximately 2 percent of Lokiarchaea’s predicted proteins. These proteins are found at similar levels in many unicellular eukaryotes. The researchers also found sequences similar to eukaryotic ESCRT genes (key components of intracellular vesicle trafficking mechanisms).

Figure source: Nature
Figure source: Nature

In an interview with “The Scientist”, researcher Ettema said, “When we first started looking at these data, we realized that this is either something very special or this is some kind of weird contamination. If we look at the genetic backbone of all the housekeeping genes, Loki is very much archaeal,” he explained. “But somewhat to our surprise, Loki ended up together with eukaryotes, meaning that they share a common ancestor.”

“If we look at the type of eukaryotic genes that Loki has, it could be that it was at a stage where it started evolving a primitive way of taking up stuff via phagocytosis,” said Ettema. “It is a modern-day organism, but it seems to tell us a bit about the steps that occurred during eukaryote origin.” Among other possibilities, “it could have started evolving a mechanism to take up things—one of those might have been alpha-proteobacteria, from which mitochondria evolved at some point,” he added.

Overall, this discovery supports the long-standing hypothesis that archaea are the ancestors of eukaryotes, and helps fill an evolutionary gap between the two groups. Nevertheless, this study will add a new archaeal phylum ‘Lokiarchaeota’ to the biology textbooks in the near future.

These findings were published in Nature.


  1. The extent to which the results of such genome research provide incontrovertible evidence is perhaps a matter of debate.

    That, of course, is not not to say it is not intriguing inasmuch it supports an incremental model rather than the singularity favored by Nick Lane and others.

    But a much stronger clue to the transition from prokaryote to eukaryote has been found by Masashi Yamaguchi et al.

    In this case the fortuitous discovery of an extant deep sea organism (Parakyron myogenensis), the morphology of which strongly suggests an intermediate.

    Both eukaryosis and abiogenesis are issues explored in my latest book as part of a far broader evolutionary process that is traceable from the formation of the chemical elements in stars right through to its latest manifestation, the emergence of the Internet. See “The Intricacy Generator: Pushing Chemistry and Geometry Uphill”