Mediocre Poison Eaters And The Imperfection of Evolution

It’s easy to forget sometimes that evolution is always a work in progress. We contemplate the eye or look upon an oak tree, and ask, how could they be any better? Somehow, in those moments of awe, we forget about detached retinas and sudden oak death. The evolutionary race is not in fact won by the perfect, but by the good-enough. And it just so happens that one of the best illustrations of evolution’s mediocrity is unfolding in front of us right now.

This episode of evolution is entirely of our own doing. In 1936, a chemical called pentachlorophenol went on the market. It was hugely popular as a way to preserve telephone poles and lumber against fungi and termites. Unfortunately, it also turned out to be toxic to humans, and once it got into the soil it could contaminate the ground for years. That’s because the molecule–five chlorine atoms decorating a ring of carbon atoms–had not previously existed in nature. Microbes had not evolved to feed on it before. It was as toxic to them as it was to us.

Starting in the 1970s,  however, scientists discovered some microbes that had begun to feed on pentachlorophenol. Pollution-eating bugs are popular in microbiology circles, because they can sometimes be deployed to clean up our messes. So a number of scientists have spent recent years dissecting the pentachlorophenol-eaters. Last year, for example, researchers published the genome of one such species, Sphingobium chlorophenolicum, which had been discovered in pentachlorophenol-laced soil in Minnesota in 1985.

When you first learn how Sphingobium eats pentachlorophenol, it inspires that same awe that eyes and oaks do. It uses a series of enzymes to pick off the chlorine atoms one at a time, like a gorilla removing spines from nettles. And yet, for all the complexity of Sphingobium‘s biochemistry, it does a pretty lousy job of feeding on pentachlorophenol.

Shelley Copley of the University of Colorado and her colleagues have tested out the individual enzymes that the bacteria use. They actually work far slower than typical enzymes involved in breaking down toxins. When they grab onto the molecule, they often lose their grip. Sometimes they grab onto an entirely different molecule instead. And while Sphingobium may be able to eat pentachlorophenol, they are not completely immune to its risks. Expose the bacteria to a high level of the pesticide, and they die.

A look at the genes that encode the enzymes reveals why they’re so mediocre: they’re new to the job. While they all act together like workers on an assembly line, they have different origins. Copley and her colleagues were able to gain some clues to those origins by comparing Sphingobium chlorophenolicum to closely related species that cannot break down pentachlorophenol. They have summed up their current understanding of the evolution of pentachlorophenol-feeding with a diagram, which I’ve reprinted below (click to enlarge). The molecules show pentachlorophenol being dismantled. The microbe’s enzymes are marked in red in each reaction arrow. (Spont. means that a reaction happens on its own–spontaneously.)

The oldest part of this pathway is marked in green. Related bacteria have PcpA and PcpE, and they use these enzymes to break down molecules that are similar to pentachlorophenol at this stage of the reactions. But the genes for the steps marked in blue and yellow were not present in that common ancestor. Instead, Sphingobium chlorophenolicum acquired them after it split off from its relatives.

Horizontal gene transfer, as this process is known, is common in the microbial world. Microbes slurp up DNA from dead neighbors, viruses shuttle genes to new hosts, and sometimes microbes even build tubes to inject their genes into other microbes. Scientists became aware of horizontal gene transfer when bacteria started trading genes for antibiotic resistance, rendering wonder drugs less than wonderful. But these cases were relatively simple: a single gene could, on its own, give bacteria better protection against antibiotics.

What’s been happening in Sphingobium is more complicated. Two sets of genes have moved into the bacteria, where they have linked together, as well as to a set of genes that was already there. Together, they took on an entirely new tasks that none of them could have handled before: breaking down pentachlorophenol.

Scientists don’t yet know where those pieces of the pentachlorophenol pathway came from, or what exactly they were doing in older microbes. PcpC, the enzyme in the yellow section, is closely related to enzymes that break down proteins. In fact, PcpC can still break down proteins, although not as well as more specialized enzymes. Breaking down proteins might have been its previous job, and only later did its ability to help break down chlorine-bearing molecules come to the fore.

The genes in this pathway have been continuing to evolve over the past few decades. Natural selection favors the microbes that can grow faster on pentachlorophenol than its competitors. But that competition has not produced any gold medalists just yet. The enzymes still aren’t very well adapted to breaking down this toxic molecule.

Consider the very first step in the pathway, where PcpB picks off the first chlorine atom. Usually, enzymes make molecules less toxic than before. But PcpB does the opposite. It turns pentachlorophenol into the truly nasty tetrachlorobenzoquinone, which you do NOT want to mess with.

There are other cases in which enzymes make molecules more toxic, rather than less. But in those cases–where evolution has had more time–the enzymes are adapted to protect the cell from their toxic creation. The molecule never gets a chance to float away, free to wreak havoc, because the enzyme binds to the next enzyme, carefully handing off the prisoner.

Sphingobium can’t do that handoff. The best it can manage is to have PcpB hold onto the molecule until the next enzyme, PcpD, happens to bump into it. That strategy keeps the nasty tetrachlorobenzoquinone from escaping and killing the microbe. But it slows down the whole process of breaking down the molecule enormously.

Will the mediocre Sphingobium evolve a hand-off? Stay tuned. If it only took a few decades for the microbe to get this far, maybe we’ll witness the next step in our lifetime.