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Evolution

From 591 leagues under the sea to eukaryote and me: introducing the closest known relative to our cells

Spang, J.H. Saw, S.L. Jørgensen, K. Zaremba-Niedzwiedzka, J. Martijn, A.E. Lind, R. van Eijk, C. Schleper, L. Guy, and T. Ettema. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 2015. Doi:10.1038/nature14447

How evolutionary biologists get around.

You might not be able to relate to a single cell organism like an amoeba, but you are in fact the sum of your differentiated eukaryotic cells. Cells on this earth come in two flavors – eukaryotic and prokaryotic. Unlike prokaryotes, eukaryotes possess compartments known as organelles that are surrounded by inner membranes and define the separation of labor within the cell. Notable among these organelles are the mitochondria that are responsible for energy generation in eukaryotic cells. Mitochondria freakishly possess their own genomes (separate from that of the DNA of the mother cell), which are highly similar to the genomes of a class of bacteria known as the alphaproteobacteria. Indeed, the “endosymbiont theory” suggests that some 2 billion years ago, approximately 1.5 billion years after the appearance of the first prokaryotes (according to the spotty fossil record), one prokaryote wandered into another prokaryote, settled, stayed, eventually lost the ability to exist on its own, and so became the specialized powerhouse of the eukaryotic cell. In the meantime, the host cell built a membrane around its own DNA to protect it from interfering with the DNA of its tenant, and so was born the nucleus of the eukaryotic cell. Now, until the 1970s, “prokaryote” was synonymous with “bacteria” until a guy named Carl Woese took a look at a highly conserved prokaryotic molecular marker known as the 16S RNA gene and determined that prokaryotes actually comprised two distinct groups –bacteria and “archaea”.

Simply speaking, two camps exist on the origin of eukaryotic life. The “three-domain” view of life championed by Woese supposes that bacteria, archaea, and eukaryotes arose out of a single common ancestor. However, the prevailing view of late is that eukaryotes emerged from an archaeon, which some think is just a highly evolved bacterium that took in another bacterium (that became the mitochondrion). Hence, the evolutionary Holy Grail, so to speak, would be a “living fossil” or an archaeon that represents a “transition form” in the continuum from archaea to bacteria, next stop eukaryote.

A recent study published in Nature by Anja Spang et al. reports evidence for such a transition form, an archaeon with “eukaryote specific signatures” more related to you and I than any prokaryote known to multicellular eukaryotic humans.

The team chanced upon this precocious archaeon while surveying deep ocean microbial diversity in the undersea vents known as Loki’s castle somewhere between Greenland and Norway. In one particular ten-gram lump of matter collected from 3,283 kilometers (about 2,000 miles) below they found that about ten percent of the 16S genes (that evolutionary marker first used by Woese) surveyed corresponded to a group of archaea known as “TACK,” the most recent known archaeal ancestors to the eukaryotes.

Really sunken treasure. Collection site of 10-gram "gravity" core analyzed in the study indicated by red dot).

Really sunken treasure. Collection site of 10-gram “gravity core” analyzed in the study (indicated by red dot labeled “GC14”). Image courtesy Nature.

Aware of the potential evolutionary implications of new TACK species, Spang et al. undertook the brave effort to “pull” genomes out of the genetic material contained in their prized ten grams of deep-sea gunk (not a lot to work with). Impressively, they were able to construct three partial genomes of archaea, which they termed “Lockiarchaeota”. Comparing “marker” proteins from all three “domains” of life, they found that the Lokiarchaeota were “monophyletic” with eukaryotes, meaning they could be the first evidence of the elusive transition form.

"Lokiarchaeota" (highlighted in red) share a common ancestor with Eukarya

All in the family. “Lokiarchaeota” (highlighted in red) share a common ancestor with Eukarya. Image courtesy Nature.

Hot on the trail of evolution, they took the most complete genome of the three, and dug deeper to see just how similar its DNA fingerprint was to that of a eukaryote. Much to their scientific delight, they found that a tantalizing 3.3 percent of the genome showed high similarity to eukaryote-specific genes. They went on to identify homologs (sequence-similar) genes encoding “actins,” which are involved in cell motility, division, and transport. Importantly, these actin-like genes more closely resembled those found in eukaryotes than in other archaea. Additionally, they found evidence for proteins known as GTPases, which are involved in transporting stuff in membrane-enclosed “vesicles”. The relative number of potential GTPase in Lokiarchaeum, about 2 percent, is consistent with what might be expected of a eukaryotic genome. Lastly, they found genes that correspond to the primitive “ESCRT” complex, which is responsible for shaping membranes in eukaryotes and “escorting” garbage out of the cell in membrane-enclosed vesicles. In short, Lokiarchaeum started to look like an advanced archaeon with the potential to engulf another cell … and make a eukaryote.

Span et al.’s survey of eukaryotic-specific signatures in Lokiarchaeum paints a picture of a highly complex ancestral “shape-shifting” archaea. The name “Loki,” in addition to indicating the sample collection site, aptly refers to a god from Norse mythology capable of assuming any shape he pleased. Nonetheless, wary evolutionary time traveler, these findings, though intriguing, must be taken with a grain of salt, as they are entirely based on a DNA fingerprint. In order to get a sense of how true to predicted form, Lokiarchaeum actually are to eukaryotes, scientists will need to isolate and study examples of their cells, dead or, better yet, alive. Perhaps one day it will be possible to cook up a eukaryotic Frankenstein in the lab, leaving one scientist declaring, “Woese is me!”

 

So, which came first, the eukaryote or the Lokiarchaeum? What do you think?

 

Further reading (and inspiration for the introductory material of this article) can be found in this excellent piece by Carl Zimmer.

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