Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [19]
E. coli has no wires that scientists can pull apart to learn how its circuits work. Instead, they must do experiments of the sort Jacob and Monod carried out. They observe how quickly the bacteria respond to their environment, how quickly they make a certain protein or clear another one away. Scientists combine the results of experiment after experiment into models, which they use to make predictions about how future experiments will turn out. The fundamental discoveries that Jacob, Monod, and others made about E. coli have led other scientists to pick apart the circuitry of other species, including us. But in the fifty years since Jacob squirmed in a cinema seat, scientists have continued to pay close attention to E. coli. They discovered intriguing patterns in E. coli’s circuitry, which they mapped out in more detail than in of any other species, and they’ve discovered that E. coli’s circuitry mimics the sort of circuitry you might find in digital cameras or satellite radios.
To prove that I’m not dabbling in idle metaphor, I want to probe the wiring of one of E. coli’s many circuits. This particular circuit controls the construction of E. coli’s flagella. It has taken the work of many scientists over many years to discover most of the genes that belong to this circuit. But in 2005, Uri Alon and his colleagues at the Weizmann Institute of Science in Rehovot, Israel, figured out what the circuit does. It acts as a noise filter.
Engineers use noise filters to block static in phone lines, blurring in images, and any other input that obscures a true signal. In the case of E. coli, the noise is made up of misleading cues about its environment. With the help of a noise filter it can pay attention only to the cues that matter. It’s important for E. coli to ignore noise when it builds a flagellum because the process is a lot like building a cathedral.
The microbe must switch on about fifty genes, which make tens of thousands of proteins. Those proteins must come together in a tightly choreographed assembly. First the motor must insert itself in the membranes. A syringe has to slide through the center of the motor, which then injects thousands of proteins into the growing tail. The proteins squirm through the hollow shaft and emerge to form its new tip. The process takes an hour or two, which for E. coli can mean several generations. A new microbe inherits a partially built tail and passes it on, still unfinished, to its descendants.
By the time E. coli has finished building these flagella, the crisis may be long over. All that energy will have gone to waste. So E. coli keeps tabs on its surroundings, and if life does seem to be getting better, it stops building its flagella. The only problem with this strategy is that a sign of better times may actually be a fleeting mirage. If E. coli abandons its flagella when a single oxygen molecule drifts by, it may end up stranded in a very dangerous place. To E. coli these false signs are noise it must filter out of its circuits.
To explain how E. coli filters out noise, I will draw a wiring diagram. An arrow with a plus sign means that a signal or a gene boosts the activity of another gene. A minus sign means that the supply of protein is reduced. The first link in this circuit is from the outside world to the inner world of E. coli. When the microbe senses danger, it sometimes responds by producing a protein called FlhDC.
FlhDC is one of E. coli’s master switches. It can latch on to many spots along E. coli’s chromosome, where it can switch on a number of genes. These genes make many of the proteins that combine to make flagella.
In this simple form, E. coli’s flagella-building circuit has a major flaw. It can turn on flagella-building genes in response to stress, but it also has to shut them down as soon as the stress goes away. Once the microbe stops making new FlhDC, the old copies of FlhDC gradually disappear. As they do, the genes FlhDC controls can no longer make their proteins. The complex assembly