Sunday, March 11, 2012

Biological Revolutions: Eucaryosis


(Picture from here.)

In the last post we talked about the world prokaryotes made.

Now we're going to talk about eukaryotes, bequeathed to us in part by the prokaryotes.

Essentially. you can consider eukaryotes as defined by their use of membranes. Think of prokaryotes as a bag of chemicals that mix, mix, mix and the resulting chemistry is what drives their lives. (Not to denigrate bacteria. The metaphor is intentionally oversimplified.)

In eukaryotes that bag is subdivided into smaller bags inside the larger one. There's a bag for DNA material (the nucleus.) A bag for energy production (the mitochondria.) A bag for photosynthesis (the chloroplast.) These are called membrane bound organelles: they're boundaried by membranes and look like little organs. The defining structure is the nucleus. Eukaryotes may or may not have the other organelles.

Right from the beginning we can see that there's a sort of specialization of the cell structure of eukaryotes. It's interesting that the more highly organized collections of cells on the planet (kelp, oaks, starfish, dolphins, us) are all made of cells that began with internal specialization.

The fundamental theory on how eukaryotes evolved were from a union between two prokaryotes creating the Last Eukaryotic Common Ancestor (LECA.) The question is how this happened.

One idea suggests that Eukarya originated when a bacteria engulfed a member of the Archaea. (See here.) Three bacteria have been implicated:
  • Planctomycetes: a phylum of aquatic bacteria. These reproduce by budding.
  • Verrucomicrobia: a recently described phylum of bacteria found in aquatic and soil environments. They are often parasitic and found in eukaryotic hosts. They may be relatives of both Chlamydiae and Planctomycetes.
  • Chlamydiae: intracellular pathogens found in a wide variety of hosts. All known species grow by infecting eukaryotic cells.
These are collectively called PVC and are not to be confused with sewer pipe.

The archeon in question may be something called thaumarchaeota, a newly proposed phylum containing only four species. These are chemotrophic organisms and may play a role in biogeology but it's too soon to tell. The thaumarchaeon provided a number of necessary proteins absent in other phylums of the Archaea and Bacteria. The PVC donated donated another of other chemicals involved in, for example, membrane chemistry that is necessary for a nucleus.

This process is called endosymbiosis: a symbiotic relationship with something inside. This isn't hard to think about. We do this all the time with the bacteria in our gut. Cattle absolutely require endosymbiosis to survive. Endosymbiosis was a possibility as soon as there were organisms that had an inside and an outside-- remember containment?

It's also quite likely that there were archaic viruses that also injected their fair share into the LECA. One scenario is the addition of these viral proteins accelerated the eukaryote drive towards complexity.

But it's never simple. There are six major eukaryotic supergroups. (See here.) If LECA was the sole ancestor of all the supergroups we'd expect there would be a lot of common ground between them. There is, of course. But there are some interesting distinctions.

The mitochondrion is a little organelle that has its own DNA and ribosomes-- this fact is the source, in fact, of the idea that eukaryotes derived from a prokaryote swallowing a neighbor. It reproduces along with the rest of the cell but does it on its own, separating its own DNA and creating daughter mitochondria. Its ribosomes are larger and more complex than ribosomes of prokaryotes. From this we can infer that LECA's mitochondrial ribosomes were also larger and more complex. LECA is the ancestor of the eukaryotic supergroups.

But the ribosomes of the supergroups are quite varied and diverse-- more than we would expect. More, in fact, than the ribosomes in the main cell or bacteria or chloroplasts. (See here.) One possibility is that viral invasions added or altered DNA differently in the mitochondria in the different supergroups. (See here.)

It gets even more interesting.

Gemmata obscuriglobus (a member of Planctomycetales) lives in fresh water and reproduces by budding. Its nuclear material has a double membrane the resembles a eukaryotic nucleus. This psuedonucleus suggests a bridge between prokaryotes and eukaryotes. (See here.) In addition, G. o. can perform endocytosis.

Endocytosis is the process of cells engulfing material and ingesting. Bacteria and Archae don't do this. Instead, they pull material into the cells through pores. G. o. appears to be able to ingest material by enclosing it in a membrane and bring the enclosed material into the cell.

Maybe G. o. is just a curiosity. Except it appears to use a set of proteins to do the job similar to the ones used by eukaryotes. Similar proteins have been found in other members of the PVC tribe.

Complicating this is the role of viruses, some of them very, very large. The Mimivirus has more DNA than a bacteria and about half that of a eukaryotic cell. Further, Mimivirus contains coding for several common proteins to the three domains of life: Bacteria, Archaea and Eukaryota. Some have considered viruses as the source of Eukarota in that a large virus could hijack a cell but get stuck before it is able to create more viruses. Instead, the cell divides using the virus DNA instead of its own. Since the virus has its own membrane it, in effect, becomes the nucleus of the cell. The other organelles were then engulfed via endocytosis.

Regardless, there's no doubt what happened next.

We few, we happy few, we band of brothers

The eukaryotes were born.

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