Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [58]
EVOLUTION ON DEMAND
When Salvador Luria discovered the jackpot pattern in E. coli’s resistance to viruses in 1942, he provided some of the first compelling evidence that mutations strike randomly and blindly. A vast number of other experiments on E. coli and many other species confirm the steady rate of mutations. But there are a few experiments on E. coli that raise some intriguing doubts. Perhaps some mutations are not so blind after all.
Floyd Romesberg, a chemist at Scripps Research Institute in La Jolla, California, carried out an experiment to watch E. coli evolve resistance to antibiotics. The drug he chose was ciprofloxacin, or cipro for short. Cipro first emerged in the early 1980s as a promising replacement for older antibiotics that had begun to fail. But within a few years, scattered reports of resistance began to appear. Cipro-resistant bacteria are now very common in some parts of the world. In Germany, 15 percent of E. coli were resistant in 2002. In China that same year, one study put the figure at 59 percent.
To understand how cipro-resistant genes evolved, Romesberg and his colleagues injected a disease-causing strain of E. coli into six-week-old mice. They then treated the mice with cipro, and the infection disappeared. Or at least it seemed to. Three days later the mice were sick with E. coli again. When the scientists tested the bacteria, they discovered that the E. coli had become fifty times more resistant to cipro since the start of the experiment.
Cipro kills E. coli by tricking it into committing suicide. It interferes with an enzyme known as a topoisomerase, which normally helps to untangle DNA by snipping it and then joining it back together. Once the topoisomerase has cut the DNA, cipro prevents it from finishing its job. The free ends attract other enzymes whose job it is to chop up loose pieces of DNA. They end up destroying much of E. coli’s chromosome and thus killing the microbe.
It occurred to Romesberg that cipro might cause E. coli to do something else as well: mutate faster. E. coli repairs damaged DNA with enzymes called polymerases. It makes two kinds of polymerases: one that does high-fidelity repair and one that does low-fidelity work. The hi-fi polymerases usually handle all the repair work while the genes for lo-fi polymerase are switched off by a protein called LexA. But things change when E. coli is in a crisis. When E. coli becomes burdened with a lot of damaged DNA, LexA falls off the lo-fi polymerase genes. Now the lo-fi polymerases help repair E. coli’s DNA. And because they do a less accurate job, they leave behind more mutations.
Romesberg wondered if these extra mutations helped E. coli evolve resistance to cipro faster. While most of the mutations might harm the bacteria, a few might produce topoisomerases that could keep doing their cut-and-paste job even in the presence of cipro. It was possible that extra mutations would arise only during these sorts of crises. Once E. coli could cut and paste its DNA again, its supply of loose DNA would dwindle. LexA would grab on to the genes for lo-fi polymerases and shut them down. E. coli would return to its more careful DNA repair.
Romesberg and his colleagues tested their hypothesis with an elegant experiment. They engineered a strain of E. coli in which LexA did not fall off the lo-fi polymerase genes. Exposed to cipro, these microbes would go on repairing their DNA with exquisite accuracy. Romesberg and his colleagues injected their engineered strain into mice and gave them cipro. In 2005, they reported their results: unable to mutate more, the E. coli evolved no resistance to cipro at all.
Romesberg’s experiment suggests that E. coli is not just passively accumulating mutations. E. coli may have evolved ways to manipulate mutations to its own advantage.
The first inklings of not-so-blind mutations came in a “water, water,