A virus with half a wing

Richard Lenski’s team is one of my favourite research groups in the whole world. If the long-term evolution experiment with E. coli was the only thing they ever did, they would already have earned my everlasting admiration. But they do other fascinating evolution stuff as well. In their brand new study in Science (Meyer et al., 2012), they explore the evolution of a novelty – in real time, at single nucleotide resolution.

For their experiments, they used a pair of old enemies: the common gut bacterium and standard lab microbe E. coli, and one of its viruses, the lambda phage. Phages (or bacteriophages, literally “bacterium eaters”) are viruses that infect bacteria. They are also some of mother nature’s funkiest-looking children. Below is an example, because if you haven’t seen one of them, you really should. I borrowed this electron micrograph of phage T4 from GiantMicrobes, where you can get a cute plushie version 😛

Phages work by latching onto specific proteins in the cell membrane of the bacterium, and literally injecting their DNA into the cell, where it can start wreaking havoc and making more viruses. Meyer et al.‘s phage strain was specialised to use an E. coli protein called LamB for attachment.

The team took E. coli which (mostly) couldn’t produce LamB because one of the lamB gene’s regulators had been knocked out. Their virus normally couldn’t infect these bacteria, but a few of the bacteria managed to switch lamB on anyway, so the viruses could vegetate along in their cultures at low numbers. Perfect setup for adaptation!

Meyer and colleagues performed a lot of experiments, and I don’t want to go into too much detail about them (hey, is that me trying not to be verbose???). Here are some of their intriguing results:

First, the phages adapted to their LamB-deficient hosts. They did so very “quickly” in terms of what we usually think of as evolutionary time scales (naturally, “evolutionary time scales” mean something different for organisms with life cycles measurable in minutes). Mutations in the gene coding for their J protein (the one they use to attach to LamB) enabled them to use another bacterial protein instead. Not all experimental populations evolved this ability, but those that did succeeded in less than 2 weeks on average.

The new protein target, OmpF, is quite similar to LamB, which might explain how the viruses evolved the ability to use it so quickly. But more interesting than the speed is the how of their innovation. Amazingly, all OmpF-compatible viruses shared two specific mutations. Another mutation always occurred in the same codon, that is, it affected the same amino acid in the J protein. A fourth mutation invariably occurred in a short region near the other three. Altogether, these four mutations allowed the virus to use OmpF. Plainly, we are dealing with more than mere convergent evolution here. Often, many different mutations can achieve the same thing (see e.g. Eizirik et al., 2003), but in this case, a very specific set of them appeared necessary. I’ll briefly revisit this point later, but first we have another fascinating result to discuss!

By comparing dozens of viruses that did and didn’t evolve OmpF compatibility, the researchers determined that all four mutations were necessary for the new ability. Three were not enough; there were many viral strains with three of the four mutations that couldn’t do anything with LamB-deficient bacteria. On the surface, this sounds almost like something Michael Behe would say (see Behe and Snokes, 2004), except the requirement for more than one mutation clearly didn’t prevent innovation here. Given the distribution of J mutations, it’s also likely that they were shaped by natural selection, even in virus populations that didn’t evolve OmpF-compatibility. So what did the first three mutations do? What use was, as it were, half a new J protein?

The answer would delight the late Stephen Jay Gould: the new function was a blatant example of exaptation. Exaptations are traits that originally had one function, but were later co-opted for another. While three mutations predisposed the J gene to OmpF-compatibility, they also improved its ability to bind its original target. Thus, there was a selective advantage right from the first mutation. And, in essence, this is what we see over and over again when we look at novelties. Fish walk underwater, non-flying dinosaurs cover their eggs with feathered arms, and none of them have the first clue that their properties would become success stories for completely different reasons.

In the paper, there is a bit of discussion on co-evolution and how certain mutations in the bacteria influenced the viruses’ ability to adapt to OmpF, but I’d like to go back to the convergence/necessity point instead. I have a few half-formed thoughts here, so don’t expect me to be coherent 😉

We’ve seen cases where the same outcome stems from different causes, like in the cat colour paper cited above. Then there is this new function in a virus that seems to always come from (almost) the same set of mutations. Why? I’m thinking it has to do with (1) the complexity of the system, (2) the type of outcome needed.

Proteins interact with other proteins through very specific interfaces. Sometimes, these interactions can depend on as little as a single amino acid in one of the partners. If you want to change something like that, there is simply little choice in what you can do without screwing everything up. On the other hand, something like coat colour in mammals is controlled by a whole battery of genes, each of which may be amenable to many useful modifications. And when it comes to even more complex traits like flying (qv. aside discussing convergence and vertebrate flight/gliding in the mutations post), the possibilities are almost limitless.

So there’s that, and there is also what you “want” with a trait. There may be more ways to break a gene (e.g. to lose pigmentation) than to increase its activity. When the selectively advantageous outcome is something as specific as a particular protein-protein interaction, the options may be more restricted again. (To top that, the virus has to stick to the bacterium with a very specific part in its structure, or the whole “inject DNA” bit goes the wrong way.) Now that I read what I wrote that sounds like there will be very few “universal laws” of evolutionary novelty (exaptation being one of them?). Hmm…

References

Behe MJ and Snoke DW (2004) Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Science 13:2651-2664

Eizirik E et al. (2003) Molecular genetics and evolution of melanism in the cat family. Current Biology 13:448-453

Meyer JR et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335:428-432

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