Molecular biology in the light of comparative genomics.

The week before last, I was at a conference at EMBL Heidelberg on Protein Synthesis and Translational control. I found it to be a stimulating, very enjoyable meeting, despite being rather disappointed by it being dominated by eukaryotic mechanisms, with only a few talks devoted to bacterial translation (and from what I remember none on organellar or archaeal translation). Translation is a universal, ancient process, and analyses of its highly conserved components have taught us much of what we know about the evolution and diversity of life on Earth. Despite that, out of ~300 (I would guess) participants, I was the only person presenting evolution stories. I wasn't selected for a talk, but I presented two posters, one on the RelA/SpoT family of ribosome-associated starvation response enzymes and one on gain and loss of mitochondrial translational initiation factors. I'm also pretty sure I was the only blogger and tweeter there too... hmm is that connected? Anyway, that's not the point here. My point is that a little evolution goes a long way in terms of predicting functions and universality of mechanisms, and it seems to me that molecular biologists aren't taking full advantage of that. There were a few talks mentioning new factors. My immediate thoughts were what are they related to? What do sequence comparisons suggest about them? Are they actually in any other organisms than yeast or humans? Model organisms are unfortunately not always representative, and we need evolutionary analyses to put results in perspective.

It's not just at this protein synthesis conference that I was the one and only molecular evolutionary biologist. Except for studies on ribosome origin, which are often low on evidence, high on speculation, and conducted by non-experts in molecular evolution (see my previous blog post), it's the same in the last few conferences I've been to. The protein synthesis field is a very active, exiting field with great people who are not afraid of bioinformatics and collaborating with bioinformaticians. Just, usually not molecular evolutionary biologists. That doesn't mean that people can't be enlightened though. After the first day, a co-attendee chatted with me about my research. He'd come across my paper of EF-G duplication and functional evolution and was excited by it. He said "I thought evolution was really boring, but actually it's interesting and very useful." He went on to propose an interesting collaborative project.

It's not that there are no published comparative genomics studies done at all in the protein synthesis field, just there are very few and though some are good, more often they are done badly (for example claiming orthology seemingly without making phylogenetic trees and getting it wrong), and with the focus on distribution without site-specific or structural analyses to make functional inferences. Specific expertise is required to do it right. The kind of expertise found in evolutionary biologists. However, the latter tend to stick to the evolution field, and it seems to me that important questions don't always get answered that way. I'm not sure, but I would hazard a guess that it's the same in other molecular mechanism fields (eg transcription, cell cycle/replication). There are lots of gaps in our knowledge about core cellular processes that need filling with the help of people competent in comparative genomics.

The scarcity of other molecular evolutionary biologists within the protein synthesis field could be considered to be an advantage for me. I have my own niche afterall, and I have no shortage of work because not all experimentalists overlook the importance of evolution. However, there are many, many more interesting proteins and and questions than I have time to look at. And I don't have a lab of minions as yet.

Here's an example of how wrong conclusions can be propagated in the absence of molecular evolution analyses. It is discussed in a paper that I'm writing up at the moment. I'll blog the full story with the real proteins named in the fullness of time, but this is just for the idea.

So, in an original paper, it was claimed that an insertion in human mitochondrial protein 1 in figure A, above compensates for the function of protein 2, present and essential in E. coli, but lost in humans. The insertion is not at all homologous to protein 2. Nevertheless, if E. coli protein 1 is modified to include the insertion usually only found in humans, protein 2, which is usually essential, becomes dispensable. So the authors of the original study claimed that the insertion evolved in eukaryotes to replace the function of protein 2. This is all very interesting, but I immediately had a question. Since protein 2 is universally absent in eukaryotes (this is already known), is the insertion universally present in eukaryotes? I think this is a very important question, which was not addressed in the original paper. Nevertheless, there has been a whole slew of other papers propagating the conclusion that the insertion evolved to take the place of protein 2. 

I was not content with an evolutionary conclusion drawn on the comparison of three organisms (the third was archaea, also missing the insertion), so I decided to answer this question myself. The result was oops. The insertion is actually only in vertebrates (see figure B, above).  So for millions of years, eukaryotes had been (and many still are) doing fine without either the insertion or protein 2. Maybe the insertion does replace the function of protein 2 in vertebrates, but there must be some other, unknown, possibly more general mechanism(s) compensating. And this is an interesting avenue worth pursuing.

That's one angle to the story, and it's a bit negative, true, but there's also a very positive angle to this particular paper that I'm writing. There is a protein 3, also universal in bacteria, and almost universal in mitochondria. It had never previously been found in yeast, however with some sensitive sequence searching (PSI-blast) I found a homologue, which I confirmed as the orthologue with phylogenetic analysis. This yeast protein 3 is very divergent though, with insertions and deletions relative to the well known ones, so whether it is the functional equivalent of protein 3 was still unknown. But that's when it becomes wonderful to be an evolutionary biologist among experimentalists, because our collaborators have been able to confirm the function of my newly identified protein in vivo.  So we have identified a new protein in yeast, essential for mitochondrial function, and a really nice evolutionary story to go along with it.

In conclusion, it's said so many times that it's becoming a nasty cliche, but Dobzansky's quote "nothing in biology makes sense except in the light of evolution" is spot on.  I would encourage experimentalists to consider whether molecular evolution can help answer some of your questions, or even raise some exciting new ones. I would also urge molecular evolutionary biologists to consider collaborating with experimentalists whenever you can, because it's so exciting and satisfying to get your predictions tested.

OK, now to finish this paper about proteins 1, 2 and 3, which I will blog about when the paper is published and available!