A Class Asks Questions...

by Yina Cobián, Alan Du, Kanika Khanna, Neeraja Vegesna, Chunghoon Woo, and Asami Yamamura

The authors were members of the 2015 UCSD/SDSU Integrative Microbiology Graduate course, organized by Doug Bartlett and Elio Schaechter.
 

In a recent class, we discussed an exciting paper about a new group of Archaea that just may be the "missing link" between prokaryotes and eukaryotes. Spang and colleagues identified a novel candidate archaeal phylum, the Lokiarchaea, which by phylogenomic analysis forms a mo­no­phy­le­tic group with eukar­yotes. Their genomes "encode an expanded repertoire of eukar­yotic signature proteins suggestive of sophisticated membrane remodeling capabilities". These organisms might have played a role in the original endosymbiosis that gave rise to the eukaryotes and their evolution.

Loki's Castle, the field of deep sea vents bet­ween Norway and Greenland, is home to sedi­ments containing DNA from the newly dis­cov­er­ed archaea. Credit R.B. Pe­der­sen/Centre for Geo­bio­logy, Bergen, Norway. The vent field was given the name Loki's Castle as its shape re­min­ded its discoverers of a fantasy castle. The re­fer­en­ce is to the ancient Norse god of fire and trickery, Loki. Source

The endosymbiotic theory of eukaryotic origin hy­po­the­si­zes that eukaryotes evolved from prokaryotes that 'endo­sym­bio­sed' other pro­kar­yo­tes. These ingested pro­kar­yo­tes are thought to have been proteobacteria and to have evolved into the present mitochondria. In keeping with this notion, mitochondrial genes are phylogenetically clo­se­ly related to those of the Rickettsiales (Al­pha­pro­teo­bac­te­ria). In a second 'big event', cyanobacteria are thought to have been 'endosymbiosed' by early eukaryotes and to have evolved into chloroplasts. But who is the pro­kar­yo­te that engulfed another prokaryote and acted as its host in the first place? Was it a lokiarchaeon?

We decided to propose what we would like to learn fur­ther about the Lokiarchaea. Here is a list of our quest­ions, and yeah!, the answers we instantly got from Thijs Ettema (TE), corresponding author of the paper we discussed in class:
 

• Can Lokiarchaea be cultured in the lab?

  TE: Currently, we are trying to extract and culture Loki cells in our lab, but this is quite cumbersome due to slow growth rates, and poor extraction efficiencies. However, we won't give up!

• If this is not yet possible, can they be retrieved from their environment so that we can have a look at them? What are they like, inside and out?

  TE: See above, even extracting Loki cells from the marine sediments is not straightforward for some reason. The fact that cellcounts in these sediments are really low does not help of course. However, if we would manage, we would of course would like to have a look under the microscope!

• What are the homologous genes for eukaryotic membrane remodeling doing here? Do their cells have some sort of endomembrane/cytoskeletal system? If so, this may give hints about the evolutionary pressure on the eukaryote precursor for developing and maintaining a high energy system.

  TE: This is a key question! We only know what these genes do in eukaryotes, and it is entirely possible that these genes have a somewhat different function in Loki. We must not forget that Loki and eukaryotes are separated by roughly 2 billion years of evolution!

• What kind of metabolism they have? How do they obtain energy? To maintain a membrane trafficking system in addition to housekeeping functions, they are likely to require more energy than the average archaea.

  TE: This we are currently looking into. Metabolically, Loki seems to be quite versatile, but for sure its metabolism is strictly anaerobic. Even if Loki would have some sort of membrane trafficking system, it is not clear how much energy it would cost to maintain such a system. We simply do not know enough about Loki...

• Not yet having mitochondria, they should have access to large energy sources they can easily access. Are these in the form of energy-rich organic matter from the environment or hydrothermal vents?

  TE: No, Loki was isolated from extremely nutrient-poor sediments. Do not forget that apart from the roughly 100 eukaryotic signature proteins (ESPs), Loki looks like a typical prokaryote. Hence, it is expected to have small cells, and is not predicted to need an excess of energy to maintain its cell.

• Do they endocytose particulate organic material for food? This would allow them to better utilize surrounding molecules in a seemingly harsh environment. It could explain why they are so abundant in the metagenomic sample.

  TE: We simply can't tell at his point. Sure, it would be interesting to speculate that Loki would have endocytotic or even phagocytotic capabilities, but currently there is no evidence for this. Compared to eukaryotes, Loki lack many genes that are involved in these processes.

• Before we can answer some of these questions, we need a better understanding of the environment that helped shape who they are. What is the chemical and physical world they live in?

  TE: Loki was isolated from deep (>3000 meter) marine sediments, at a depth of 75 cm below sea floor. The temperature at this location was very cold, even around freezing point! Also, as indicated above, deep marine sediments are typically very nutrient poor, and in this case also anoxic. Clearly, Loki is living a tough life!