More from Lenski's Lab, Still Spinning Furiously
Recently a new paper by Richard Lenski and colleagues (Meyer et al. 2012) appeared in Science with, as usual, commentary in the New York Times. Lenski's lab must own a red phone with a direct line to the Gray Lady.
The gist of the paper is that a certain bacteriophage (a virus that infects bacteria) called "lambda" gained the ability to bind a different protein on the surface of its host, the bacterium E. coli, than the protein it usually binds. The virus has to bind to the cell's surface as a prelude to invading it. The protein it normally binds is called LamB. Lenski's lab, however, used a bacterial strain that had turned off the production of LamB in 99% of E. coli cells but, crucially, 1% of cells still produced the protein.
Thus the virus could still invade some cells, reproduce, and not go extinct. Under these conditions the viral binding protein (called "J") underwent several mutations, apparently to better bind LamB in the fewer cells that produced it. Then, surprisingly, after the viral gene gained a fourth mutation, the viral J protein acquired the ability to bind a different protein on E. coli, called OmpF. Now the virus could use OmpF as a platform for invading the cell. Since all cells made OmpF, the virus was no longer restricted to invading just the 1% of cells that made LamB, and it prospered. The workers repeated the experiment multiple times, and frequently got the same results.
As always, the work of the Lenski lab is solid and interesting, but is spun like a top to make it appear to support Darwinian evolution more than it does. As the authors acknowledge, this is certainly not the first time a lab has evolved a virus to grow on a different strain of host. In a recent review (Behe 2010) there is a section entitled "Evolution Experiments with Viruses: Adapting to a New Host" discussing just that topic.
In general, viruses have been shown to be able to adapt to bind to related host cells that have similar surface features. In almost all cases the virus uses the same binding protein, and the same (mutated) binding site to attach to the new host cell. This also seems to be the case with Lenski's new work. As stated above, the first several mutations apparently strengthen the ability of the J protein to bind to the original site, LamB, while the fourth mutation allows it to bind to OmpF.
As the authors state, however, the mutated viral J protein can still bind to the original protein, LamB, which strongly suggests the same binding site (that is, the same location on the J protein) is being used. It turns out that both LamB and OmpF have similar three-dimensional structures, so that strengthening the binding to one fortuitously led to binding to the other.
In my review (Behe 2010) I discussed why this should be considered a "modification of function" event rather than a gain-of-function one. The bottom line is that the results are interesting and well done, but not particularly novel, nor particularly significant.
To me, the much more significant results of the new paper, although briefly mentioned, were not stressed as they deserved to be. The virus was not the only microbe evolving in the lab. The E. coli also underwent several mutations. Unlike for lambda, these were not modification-of-function mutations -- they were complete loss-of-function mutations.
The mechanism the bacterium used to turn off LamB in 99% of cells to resist initial lambda infection was to mutate to destroy its own gene locus called malT, which is normally useful to the cell. After acquiring the fourth mutation the virus could potentially invade and kill all cells. However, E. coli itself then mutated to prevent this, too. It mutated by destroying some genes involved in importing the sugar mannose into the bacterium. It turns out that this "mannose permease" is used by the virus to enter the interior of the cell. In its absence, infection cannot proceed.
So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.
Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and "The First Rule of Adaptive Evolution." Quarterly Review of Biology 85: 1-27.
Meyer, J. R., D. T. Dobias, J. S. Weitz, J. E. Barrick, R. T. Quick et al. 2012 Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335: 428-432.
Photo credit: billaday/Flickr.