The Origins of Eukaryotes: Metagenomic insight into early evolution

The origins of the eukaryotic cell is one of the big puzzles of cell biology. While it has been known for a long time that the eukaryotes are more closely related to the Archaea than to the Bacteria, the ancestor of the eukaryotes has remained elusive. A new metagenomics study in Nature identifies into a possible ancestor phylum: Lokiarchaeota, or ‘Loki’ for short.

The authors were surveying microbial diversity in deep marine sediments around hydrothermal vents in the arctic. Using a metagenomic approach, they extracted DNA from sediments and sequenced 16S rRNA fragments, and found Archaea-like sequences that had not been previously isolated, indicating the presence of a novel group of organisms. They then sequenced a larger set of sequences, which allowed them to assemble the genome of this novel organism Lokiarchaeum with 92% coverage. Interestingly, there was enough sequence similarity between the Loki genome and eukaryotic genomes to suggest that there may be a common ancestor of Loki and the eukaryotes. This would alter our view of the tree of life, as shown in the image below:

Image source: http://www.sciencemag.org/content/348/6235/615.full

Perhaps more interesting than the overall sequence similarity is the finding that Loki contains sequences very similar to those of actin. Loki also contains sequences for small GTPases, which are common eukaryotic proteins involved in cytoskeleton remodelling, vesicle transport and signalling. A dynamic actin-based cytoskeleton is one of the characteristic hallmarks of eukaryotes, therefore the presence of these proteins in Loki suggests that actin pre-dates the evolution of the eukaryotes, in contrast to previous models of eukaryotic origins. However, at the moment we only have sequence information to go on – in order to observe the cytoskeleton and confirm this tantalising hypothesis we would need to isolate and culture Loki, which may be very challenging technically.

The identification of such a complex Archaebacterium is potentially a very significant discovery, and changes our models of eukaryote evolution. However there are a relatively small number of genes that the study relies on, and without isolation of the cells themselves this study relies entirely on sequence data so must be treated with caution. However, if Loki cells are identified and do turn out to be as complex as the sequences suggest this will be an incredibly important discovery for evolutionary biologists, and may help solve the mystery of the origins of the eukaryotes.

Reference: Complex archaea that bridge the gap between prokaryotes and eukaryotes. Spang et al. (2015) Nature. DOI: 10.1038/nature14447

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