Complex archaea that bridge the gap between prokaryotes and eukaryotes

Abstract

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

Figure 1. Identification of a novel archaeal lineage

a, Bathymetric map of the sampling site (GC14; red circle) at the Arctic Mid-Ocean Spreading Ridge, located 15 km from Loki’s Castle active vent site. b, 16S rRNA amplicon-based assessment of microbial diversity in GC14. Bars on the left represent the fraction of the respective prokaryotic taxa and bars on the right depict archaeal diversity. Numbers refer to operational taxonomic units for each group. MHVG, Marine Hydrothermal Vent Group; DHVEG-6, Deep-sea Hydrothermal Vent Euryarchaeota Group 6; MBG-A and -B, Marine Benthic Group A and B. c, Maximum-likelihood phylogeny of the archaeal 16S rRNA reads (see b), revealing that DSAG sequences cluster deeply in the TACK superphylum. Numbers between brackets indicate relative abundance (%) of each group relative to total and archaeal reads, respectively. MCG, Miscellaneous Crenarchaeota Group; MHVG, Marine Hydrothermal Vent Group. d, Maximum-likelihood phylogeny of 16S rRNA gene sequences indicating that the DSAG operational taxonomic unit (red font) belongs to the DSAG γ cluster. Bootstrap support values above 50 are shown. c, d, Scale indicates the number of substitutions per site.

Figure 2. Metagenomic reconstruction and phylogenetic analysis of Lokiarchaeum

a, Schematic overview of the metagenomics approach. BI, Bayesian inference; ML, maximum likelihood. b, Bayesian phylogeny of concatenated alignments comprising 36 conserved phylogenetic marker proteins using sophisticated models of protein evolution (Methods), showing eukaryotes branching within Lokiarchaeota. Numbers above and below branches refer to Bayesian posterior probability and maximum-likelihood bootstrap support values, respectively. Posterior probability values above 0.7 and bootstrap support values above 70 are shown. Scale indicates the number of substitutions per site. c, Phylogenetic breakdown of the Lokiarchaeum proteome, in comparison with proteomes of Korarchaeota, Aigarchaeota (Caldiarchaeum) and Miscellaneous Crenarchaeota Group (MCG) archaea. Category ‘Other’ contains proteins assigned to the root of cellular organisms, to viruses and to unclassified proteins.

Figure 3. Identification and phylogeny of small GTPases and actin orthologues

a, Maximum-likelihood phylogeny of 378 aligned amino acid residues of actin homologues identified in Lokiarchaeum and in the LCGC14AMP metagenome, including eukaryotic actins, ARP1–3 homologues and crenactins. Consecutive numbers in brackets refer to the number of sequences in a respective clade from LCGC14AMP and Lokiarchaeum, respectively. b, Relative amount of small GTPases (assigned to IPR006689 and IPR001806) in the Lokiarchaeum genome in comparison with other eukaryotic, archaeal and bacterial species. Numbers refer to total amount of small GTPases per predicted proteome. c, Maximum-likelihood phylogeny of 150 aligned amino acid residues of small Ras- and Arf-type GTPases (IPR006689 and IPR001806) in all domains of life. Numbers in brackets refer to the number of sequences in the respective clades. a, c, Sequence clusters comprising Lokiarchaeum and/or LCGC14AMP sequences (red), eukaryotes (blue) and Bacteria/Archaea (grey) have been collapsed. Bootstrap values above 50 are shown. Scale indicates the number of substitutions per site.

Figure 4. Identification of ESCRT components in the Lokiarchaeum genome

a, Schematic overview of ESCRT gene clusters identified in Lokiarchaeum and Loki2/3. Intensity of shading between homologous sequences is correlated with BLAST bit score. b, Maximum-likelihood phylogeny of 207 aligned amino acid residues of ESCRT-III homologues identified in Lokiarchaeum, LCGC14AMP and other archaeal lineages. Eukaryotic homologues include the two distantly related families Vps2/24/46 and Vps20/32/60. Bootstrap support values above 50 are shown. c, Maximum-likelihood phylogeny of 388 aligned amino acid residues of AAA-type Vps4 ATPases including representatives for each of the four major eukaryotic sub-groups (membrane scaffold protein (MSP), katanin, spastin/fidgetin and Vps4) as well as homologues identified in the Lokiarchaeum genome, in LCGC14AMP and in sequenced archaeal genomes. Bootstrap support values below 45 are not shown. b, c, Scale indicates the number of substitutions per site. Numbers in brackets refer to the number of sequences in the respective clades.

Figure 5. The complex archaeal ancestry of eukaryotes

Schematic overview of the distribution of ESPs in major archaeal lineages across the tree of life. Each ESP is depicted as a coloured circle and losses are indicated with a cross. Patchy distribution and absence of a particular ESP in archaeal phyla is indicated by half-shaded and white circles, respectively. ^aWhile eukaryotes and Lokiarchaeota contain bona fide actins, other archaea encode the more distantly related Crenactins. ^bOnly few members of the Thaumarchaeota contain distantly related homologs of tubulins (ar-tubulins). ^cThaum-, Aig- and some Crenarchaeota contain distant homologues of ESCRT-III (SNF7 domain proteins).