Relevant to eukaryote origins: SNARE-like proteins found in archaea

SNARE proteins control fusion of membranes in eukaryotes. These proteins are strongly conserved among eukaryotes, in key patterns: there are four main families of SNAREs, with multiple members of each family, and the conservation is not only between lineages but it is between particular kinds of membranes (and cell compartments). Since membrane structures are the hallmark of eukaryotes, the origins of SNAREs are of interest to anyone curious about the origins of eukaryotes from non-eukaryotic ancestors.

Really interesting new paper in Current Biology asks this big question:

Moreover, as all four basic SNARE types are related, it is conceivable that the first QabcR unit arose by gene duplication from one common SNARE ancestor that may have assembled into homomeric bundles. But do such prototypic SNARE proteins still exist? We therefore searched for SNARE-like sequences in prokaryotes.

They find SNARE-like proteins in archaeans and show that these proteins can interact with eukaryotic SNAREs, forming the basic large-scale complexes that are typical of eukaryotic SNAREs. The results strongly suggest that an archaean lineage does in fact contain “prototypic SNARE proteins.”

The paper leaves one really big tantalizing question unanswered, as the authors explain in the last sentence of the abstract:

A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N -ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.

It’s a clear and interesting paper, worth reading for the SNARE result but also for a nice overview of this archaean lineage, the Asgard lineage, and how much more we might expect to learn about eukaryotic origins by studying it. Here is a simple tree from their last figure, showing where that lineage fits:

PDF on request; the paper is open access (“free featured article”) during July.

https://www.cell.com/current-biology/fulltext/S0960-9822(20)30576-5

5 Likes

Is there any examples of convergent evolution of function in this lineage?

Do you mean the Asgard lineage? I don’t know but I would assume there has to be.

1 Like

The list of eukaryote-like proteins found in the asgard archaea keeps growing.

Just as in the paper @sfmatheson linked in the op, here they also show than the archaeal proteins functionally interact with their eukaryotic counterparts.

Phylogenetic analysis shows that Asgard Vps4, Vps2/24/46, and Vps20/32/60 are closely related to their eukaryotic counterparts. Molecular dynamics simulation and biochemical assays indicate that Asgard Vps4 contains a eukaryote-like microtubule-interacting and transport (MIT) domain that binds the distinct type 1 MIT-interacting motif and type 2 MIT-interacting motif in Vps2/24/46 and Vps20/32/60, respectively. The Asgard Vps4 partly, but much more efficiently than homologs from other archaea, complements the vps4 null mutant of Saccharomyces cerevisiae, further supporting the functional similarity between the membrane remodeling machineries of Asgard archaea and eukaryotes. Thus, this work provides evidence that the ESCRT complexes from Asgard archaea and eukaryotes are evolutionarily related and functionally similar. Thus, despite the apparent absence of endomembranes in Asgard archaea, the eukaryotic ESCRT seems to have been directly inherited from an Asgard ancestor, to become a key component of the emerging endomembrane system.

Then there’s this:

One could go on and on.

1 Like