A Switch is Born

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The language of DNA is written in a four-letter alphabet. The four different chemical units of DNA (called nucleotides) create an incomprehenisbly vast range of possibility codes. Consider a short sequence of 41 nucleotides. There are over 4.8 trillion trillion possible sequences it could take. In this vast universe of possibilities, how can natural selection hit on new DNA sequences that help life survive?

All living things have genes. Enzymes read those genes and produce a copy of their code, which a cell can then use to build a protein. But in order to read a gene, the enzymes must first lock onto a distinctive segment of DNA near the gene, known as a promoter. Promoters act like switches, which a cell can use to turn genes on and off. Different genes carry different promoters, so that they can be switched on under different conditions.

Scientists have studied the promoters of the bacteria Escherichia coli more closely than those of any other species, and they’ve identified some of its switching patterns. When Escherichia coli is growing quickly, it produces a lot of gene-reading enzymes factors called sigma 70. Sigma 70 can switch on several hundred genes that allow the microbe to feed and build up its biomass and reproduce. If Escherichia coli begins to starve, it slips into a sort of suspended animation, and produces a different enzyme factor called sigma S. Sigma S recognizes a different set of genes that begin to make the proteins necessary for shutting the microbe’s operations down.

Here we have a wonderfully precise system for controlling genes. Now imagine that Escherichia coli acquires a gene with no promoter at all–just a random sequence of DNA next to the gene, 41 nucleotides long. Imagine that this DNA starts going through cycles of mutation and natural selection. Would it be possible for a random sequence to change into one Sigma 70 could grab? Could it go from nothing to a promoter?

The answer is yes. How long would it take? According to some recent experiments, two days. Two.


I came across these experiments this week during my research for my next book on Escherichia coli. I’ve been learning about the long tradition of evolutionary experiments on this marvelous bug. This new promoter experiment was carried out by Shumo Liu of NEC Laboratories and Albert Libchaber of Rockefeller University and published in the Journal of Molecular Evolution.

The gene they studied provides resistance to the antibiotic chloramphenicol. The researchers inserted the gene onto a small loop of DNA called a plasmid. Bacteria often carry plasmids along with their chromosome, and they sometimes donate a plasmid to another microbe. Like other genes, genes on plasmids typically come with promoters. But Liu and Libchaber engineered their plasmids so that in the place of a promoter, the resistance genes had a random, nonfunctional sequence of DNA.

The researchers then put this DNA through some of the essential steps of evolution: mutation, selection, and replication. They made copies of the DNA and introduced mutations into some of them at random. They ran the experiment several times with different mutation rates, ranging from 18% down to .4%. They inserted the mutated DNA back into the plasmids and inserted the plasmids into Escherichia coli. The microbes were allowed to grow rapidly for 12 hours, producing a lot of sigma 70. The scientists then added a poison pill to their feast: a dose of chloramphenicol. Later, Liu and Libchaber scraped off some of the surviving bacteria from the dishes and extracted their plasmids. They introduced more mutations into the DNA, and then repeated the cycle.

Natural selection favored mutants that had stretches of DNA that sigma 70 could grab onto, even if the fit was lousy. If a microbe could produce even a little resistance to the antibiotic, it could survive better than ones that could not. Mutations that produced a better fit would switch on the resistance gene more and give microbes an even bigger evolutionary edge over other microbes.

The scientists were surprised to find that even at the lowest rate of mutation (.4%), it took only three cycles for turn a non-functional sequence of DNA into a full-blown sigma-70 promoter. The promoter made the bacteria so resistant that most of them could withstand a high dose of chloramphenicol. Liu and Libchaber only need a small population to produce these promoters–about a million strong, a thousandth the size of the population of Escherichia coli found in your own gut. When Liu and Libchaber sequenced these evolved promoters, they discovered that the DNA had converged on many of the same elements found in natural sigma 70 promoters.

The scientists caution that their results do not reproduce the precise details of evolution outside the laboratory….

In general, evolution in nature involves a large population over a long period of time and is constrained by certain historical conditions, many of which may forever be obscure. In contrast, the experimental evolution course is very short, the population size is small, and the mutation frequency is usually elevated in order to accelerate the process. Nevertheless, the experiments capture the essence of evolution; they are an iteration of mutation, selection, and replication. Experimental evolution permits us to adjust individually the parameters and repeat the process under controlled conditions, and thus, it lets us observe some essential features in the process and test certain hypotheses. In this way, molecular evolution is a bridge between the purely mathematical modeling and the ”real world” in nature.

It also lets us watch life defy the odds, day by day.

Update: Thanks to Dr. Jim Hu for some clarifications in the comments.