The nature of our last common ancestor: simple and streamlined or complex and flabby?

What is the ancestor of all life on Earth? It's one of the biggest questions in Biology... no, in Science... no in Life. I may be biased, being an evolutionary biologist, but I'm pretty sure that along with the origin of the universe, and the nature of consciousness, it's one of the biggies.

The name of this legendary ancestral creature is LUCA (I have Suzanne Vega singing in my head now), which stands for the Last Universal Common Ancestor.

Bacteria, Archaea or Eukaryote?

So what sort of creature was LUCA? There are three main types of organisms alive today: eukaryotes, bacteria and archaea. The latter two can be grouped together under the name prokaryotes, which are all single celled organisms with diverse habitats from the human gut to deep sea vents. We are eukaryotes, and eukaryotes whether multicellular like us, or single cellular like the malaria parasite Plasmodium, are on the whole more "complex" than prokaryotes. We tend to have a wider range of molecules in our cells that interact in more ways, forming larger interaction networks. Most known eukaryotes also have mitochondria, enslaved highly reduced bacteria that provide the extra energy we need to be so complex.

Figure from M Gouy & M Chaussidon Nature 451 (2008)

 So it is natural to expect that prokaryotes came first, and eukaryotes later (most likely from archaea rather than bacteria, but the relationship between eukaryotes and archaea is a very contentious one, so I will gloss over it for now, and maybe discuss later in another blog post). It is possible to test the nature of LUCA, by looking at the genes that are conserved among prokaryotes and eukaryotes. If the hypothesis is that LUCA was a prokaryote, the expectation is that the types of proteins in common among prokaryotes and eukaryotes would most resemble those of prokaryotes. In 2007, this question was addressed by Chuck Kurland et al., using so called fold superfamilies or FSFs. These are classifications of proteins, based on their three dimensional structures. This study found that, surprisingly, "the genomes of the last common ancestor (LUCA) encoded a cohort of FSFs not very different from that of modern eukaryotes."

Numbers of FSFs from 19 genomes of eukaryotes, archaea and bacteria. Figure from C.G. Kurland et al.  Biochimie 89 (2007)

"What? How can LUCA be so complex?" I hear you asking. "Doesn't that suggest intelligent design?" Well, the answer is very simple - LUCA herself was the result of many years of evolution, natural selection and extinction. No god-like designer required. A common misconception is that the last common ancestor is the first organism on Earth. In fact, LUCA is simply the only organism we can trace back to given the tiny fraction of lineages that are extant today. A hell of a lot of evolution went on before her, and in parallel to her, as well as after her. So it's possible that LUCA was surprisingly complex, something approaching a single celled eukaryote (although without the mitochondria, that would be quite a paradox). A question that then arises is "how come prokaryotes are so simple then?" Well, actually, prokaryotes may seem simple in that they have very few genes compared to eukaryotes, but in fact reduced complexity is not an easy thing to achieve. They have become streamlined in order to fill their particular niche, which may involve fast reproduction, aided by having small genomes. "Simple" organisms are often just highly specialised and economical in contrast to the flabbyness of eukaryotes with all their complex networks of molecular interactions, which enable them to outperform prokaryotes in their particular niches.

Here's a silly analogy. If they were travelers, bacteria and archaea would be backpackers, packing light for speed and ease of getting around. You never know when you might have to run for a train afterall, and you really don't want to have to pay for excess baggage when you're flying here and there. Eukaryotes on the other hand are those travellers dragging huge suitcases, packing everything they think they might need just in case, hairdryers, snacks, guidebooks, their own mini prokaryotes (mitochondria) etc etc. They didn't neccessarily put as as much effort as the prokaryotes into figuring out the absolute minimum required to survive, so some of the extra stuff is perhaps unnecessary, but some is very, very useful and allow them to flourish in situations where the prokaryotes get left behind. So they get along just as well as the prokaryotes, but in a different way.

By now you may have accepted that LUCA was a pretty cool, advanced creature, almost like a raptor or Professor Brian Cox in fact. Now though, I will be contrary and burst that bubble. There's one very important possible reason why protein fold superfamilies are present across the tree of life: horizontal gene transfer. We like to think that on the whole, genes are inherited vertically from parent to child every generation, and for multicelluar organisms, this is definitely the case. It's rather a relief too, to know that by shaking hands with an acquaintance, patting a dog or eating a bacon sandwich, you probably won't be picking up genes that will pass to your offpring. But for single celled organisms, particularly prokaryotes, horizontal gene transfer or HGT is rampant. So it is hard to be be sure that protein folds in common among all domains of life haven't just snuck in through the back door, so to speak, possibly with the help of viruses. LUCA may have been rather simple after all.

There are lots of things we don't know about LUCA. We can't even be sure that she had a DNA rather than RNA genome. For now, the mysterious LUCA is still slightly beyond our reach. But with more genomes being sequenced, particularly from unusual non-culturable organisms, maybe it will be possible to more precisely sort out the horizontal from the vertical transfers, and our picture of LUCA will become a little less obscure.

Kurland, C., Canbäck, B., & Berg, O. (2007). The origins of modern proteomes Biochimie, 89 (12), 1454-1463 DOI: 10.1016/j.biochi.2007.09.004
Lane N, & Martin W (2010). The energetics of genome complexity. Nature, 467 (7318), 929-34 PMID: 20962839