you're reading...


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.


No comments yet.

Post a Comment


  • by oceanbites 2 months ago
    Happy Earth Day! Take some time today to do something for the planet and appreciate the ocean, which covers 71% of the Earth’s surface.  #EarthDay   #OceanAppreciation   #Oceanbites   #CoastalVibes   #CoastalRI 
  • by oceanbites 3 months ago
    Not all outdoor science is fieldwork. Some of the best days in the lab can be setting up experiments, especially when you get to do it outdoors. It’s an exciting mix of problem solving, precision, preparation, and teamwork. Here is
  • by oceanbites 4 months ago
    Being on a research cruise is a unique experience with the open water, 12-hour working shifts, and close quarters, but there are some familiar practices too. Here Diana is filtering seawater to gather chlorophyll for analysis, the same process on
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  on  #oceanbites  we are featuring Hannah Collins  @hannahh_irene  Hannah works with marine suspension feeding bivalves and microplastics, investigating whether ingesting microplastics causes changes to the gut microbial community or gut tissues. She hopes to keep working
  • by oceanbites 5 months ago
    Leveling up - did you know that crabs have a larval phase? These are both porcelain crabs, but the one on the right is the earlier stage. It’s massive spine makes it both difficult to eat and quite conspicuous in
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring Cierra Braga. Cierra works ultraviolet c (UVC) to discover how this light can be used to combat biofouling, or the growth of living things, on the hulls of ships. Here, you
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Elena Gadoutsis  @haysailor  These photos feature her “favorite marine research so far: From surveying tropical coral reefs, photographing dolphins and whales, and growing my own algae to expose it to different
  • by oceanbites 6 months ago
    This week for  #WriterWednesday  on Oceanbites we are featuring Eliza Oldach. According to Ellie, “I study coastal communities, and try to understand the policies and decisions and interactions and adaptations that communities use to navigate an ever-changing world. Most of
  • by oceanbites 6 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Jiwoon Park with a little photographic help from Ryan Tabata at the University of Hawaii. When asked about her research, Jiwoon wrote “Just like we need vitamins and minerals to stay
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring  @riley_henning  According to Riley, ”I am interested in studying small things that make a big impact in the ocean. Right now for my master's research at the University of San Diego,
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Gabby Stedman. Gabby is interested in interested in understanding how many species of small-bodied animals there are in the deep-sea and where they live so we can better protect them from
  • by oceanbites 7 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Shawn Wang! Shawn is “an oceanographer that studies ocean conditions of the past. I use everything from microfossils to complex computer models to understand how climate has changed in the past
  • by oceanbites 7 months ago
    Today we are highlighting some of our awesome new authors for  #WriterWednesday  Today we have Daniel Speer! He says, “I am driven to investigate the interface of biology, chemistry, and physics, asking questions about how organisms or biological systems respond
  • by oceanbites 8 months ago
    Here at Oceanbites we love long-term datasets. So much happens in the ocean that sometimes it can be hard to tell if a trend is a part of a natural cycle or actually an anomaly, but as we gather more
  • by oceanbites 8 months ago
    Have you ever seen a lobster molt? Because lobsters have exoskeletons, every time they grow they have to climb out of their old shell, leaving them soft and vulnerable for a few days until their new shell hardens. Young, small
  • by oceanbites 9 months ago
    A lot of zooplankton are translucent, making it much easier to hide from predators. This juvenile mantis shrimp was almost impossible to spot floating in the water, but under a dissecting scope it’s features really come into view. See the
  • by oceanbites 9 months ago
    This is a clump of Dead Man’s Fingers, scientific name Codium fragile. It’s native to the Pacific Ocean and is invasive where I found it on the east coast of the US. It’s a bit velvety, and the coolest thing
  • by oceanbites 10 months ago
    You’ve probably heard of jellyfish, but have you heard of salps? These gelatinous sea creatures band together to form long chains, but they can also fall apart and will wash up onshore like tiny gemstones that squish. Have you seen
  • by oceanbites 11 months ago
    Check out what’s happening on a cool summer research cruise! On the  #neslter  summer transect cruise, we deployed a tow sled called the In Situ Icthyoplankton Imaging System. This can take pictures of gelatinous zooplankton (like jellyfish) that would be
  • by oceanbites 11 months ago
    Did you know horseshoe crabs have more than just two eyes? In these juveniles you can see another set in the middle of the shell. Check out our website to learn about some awesome horseshoe crab research.  #oceanbites   #plankton   #horseshoecrabs 
WP2Social Auto Publish Powered By : XYZScripts.com