NFtOS 1:Are you a heterokaryon?

Today's question is whether all your genes are yours. It's a more complex question than it looks, but we have some history to deal with.

I think we can pretty much all agree that prokaryotic cells (bacteria and things without those pesky organelles) are more ancestral in the grand scheme of life than eukaryotic cells (with a nucleus, mitochondria and sometimes plastids). Based on that, we can probably agree that prokaryotes evolved earlier and were the earliest form of life as we know it on our planet. There's lots of data to back this up that I won't get into here, but you can search it out if you think I'm making shit up. The two big questions in the biology of organisms way back when, are 1) how did the first cells evolve, and 2) how did we get from prokaryotic cells roaming the Earth to the first eukaryotic cell? At the moment, we just don't know. There are lots of hypotheses out there, but in the current state of science the question of how the nucleus came to be and the origin of the genetic material that now inhabits this organelle are merely questions we can argue over. I happen to think we will someday be able to explain the phenomenon, but we're stuck at the moment.

An aside here. If you are reading this and thinking that the solution has anything to do with a divine being of any kind, it's time for us to part ways. Seriously. I'm sure there are blogs out there on fairies and imaginary friends you can talk to at night, but we're not having that conversation.

Though theories on the origin of the nucleus abound, we know considerably more about the origin of the other organelles in eukaryotic cells. It turns out the plastid (aka, chloroplast) evolution is a complex mess involving (probably) one instance where a cyanobacterium (photosynthetic bacterium) was engulfed by a eukaryotic cell, but never digested. Over time, the cyanobacterium and host cell learned to live together to their mutual benefit and, as often happens in these situations, the cyanobacterial symbiont became reduced over generations and time to the point where it became obligately bound to the host cell. Once this was established, eukaryotes spent the time between then and now swapping plastids around like lice in a daycare.

The case of mitochondria is very different. The mitochondrion became part of the eukaryotic cell in the same way the plastid did, but much earlier on. In the late 1980's it was thought that there were organisms that did not contain mitochondria and that they were the most primitive eukaryotes. Since then, it has been shown that the position of those organisms in the tree of life was an artifact and that eukaryotes don't entirely lose mitochondria. Ever. Mitochondria got in once and they got in early. So early that there is no evidence of any eukaryote that lived prior to mitochondria.

But here's the kicker folks. We think that the ancestor of mitochondria belonged to the group we know know as the alpha-proteobacteria. Current day alpha-proteobacteria have good sized genomes with a couple thousand genes to make the proteins they need and we have no reason to believe that the ancestral proto-mitochondrion needed fewer genes than current day ones. However, modern mitochondria have anywhere from 0 to less than 100. In fact, almost all animal mitochondrial genomes have only 13 protein coding genes, which is another reason my animals are really damn boring, but that's for another day. So, what happened to all those bacterial-turned-mitochondrial genes? If the genome came in with a few thousand and now has, in the case of animals, 13, where are the rest?

That question brings us back to the topic of the day. It turns out that while many of the "missing" genes have been ditched because they were no longer needed in the cell's new role as a mitochondrion, 13 proteins are not nearly enough to run the mitochondrion. Rather than make the proteins in the mitochondrion from it's own genes, it has out-sourced that job to the nucleus. The vast majority of genes that make mitochondrial proteins are encoded on the nuclear genome and the proteins find their way through a complex targeting pathway. But, what should be the interesting thing here is that these genes have all been transferred from a prokaryotic cell and incorporated into the eukaryotic nuclear genome. Many of these genes are identifiable in phylogenies based on the sequence affinity to prokaryotes that they have retained, but some have been part of the eukaryote for so long that they just blend in. Therefore, the typical eukaryotic genome is home to thousands of genes that have bacterial origins and many of which perform cellular functions unrelated to the mitochondrion because they have replaced the canonical copy or they have assumed a novel function in the cell. So, in addition to the recent estimate that humans carry more bacterial cells than human cells, we also carry a decent number of bacterial genes in our genomes.