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2008

Expressing Our Individuality, the Way E. Coli Do
The New York Times, April 22, 2008
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Adapted from Carl Zimmer’s new book Microcosm: E. coli and the New Science of Life

We humans differ from one another in too many ways to count. We are shy and bold, freckled and pale, truckers and hairdressers, Buddhists and Presbyterians. We get cancers in the third grade and live for a century. We have fingerprints.

Scientists have only a rough understanding of how this diversity arises. Some of it stems from the different experiences we have, from our time in the womb on through childhood and into our mature years. These molding influences include things like the books we read and the air we breathe. Our diversity also stems from our genes--the millions of typographical differences between one genome and another.

We put a far bigger premium on nature than nurture when it comes to our individuality. That’s one reason why reproductive cloning inspires so much horror. If genes equal identity, then a person carrying someone else’s DNA has no distinct self.

But there’s a deep flaw in this way of thinking, one that blinds us to how biology--human or otherwise--really works. A good counterexample is E. coli, a species of bacteria that lives harmlessly in every person’s gut by the billions. A typical E. coli contains about 4,000 genes (we have about 20,000). Feeding on sugar, the microbe grows till it is ready to split in two. It makes two copies of its genome, almost always managing to produce perfect copies of the original. The single microbe splits in two, and each new E. coli receives one of the identical genomes. These two bacteria are, in other words, clones.

Surely, then, E. coli must be all nature and no nurture. A colony descended from a single E. coli ancestor is just a billion identical cousins, all responding to the world with the same set of genes.

Yet as plausible as this sounds, it’s far from the truth. A colony of genetically identical E. coli is, in fact, a mob of individuals. Under identical conditions, they will behave in different ways. They have fingerprints of their own.

If two genetically identical E. coli are swimming side by side, for example, one may give up while the other keeps spinning its corkscrew-shaped tails. To gauge E. coli’s stamina, the late biologist Daniel Koshland once glued genetically identical bacteria to a glass cover slip. They floated in water, tethered by their tails. Dr. Koshland offered the bacteria a taste of aspartate, an amino acid that attracts them and motivates them to swim. Stuck to the slide, the bacteria could only pirouette. Dr. Koshland found that some E. coli clones twirled for twice as long as others.

E. coli expresses its individuality in many other ways, as well. Under identical conditions, some clones cover themselves in sticky hairs that let them stick to host cells, while others remain bald. Feed a colony of E. coli lactose (the sugar in milk), and some will respond by slurping it up through special channels and digesting it with special enzymes. Others will turn up their microbial noses.

These quirks of E. coli’s personality can mean the difference between life and death for the bacteria. In times of stress, some members of a colony respond by building thousands of toxin molecules and then burst open, killing off the unrelated E. coli around them. Their fellow clones survive, though, and thrive without the competition.

Certain viruses slip into E. coli through one of the many kinds of channels in its membrane. In a colony of genetically identical bacteria, some may be covered with these channels like pincushions. Others have none at all. The viruses will kill the vulnerable clones, while the other clones live on.

E. coli’s quirks can be a matter of life and death for us, as well. Some strains cause infections in the gut, the bladder, the blood and even the brain. In many cases, doctors try to kill the bacteria with antibiotics, which jam up the normal workings of their genes and proteins. In a susceptible colony of E. coli, a strong antibiotic will kill most of the bacteria, but not all of them. Some will survive.

The survivors escape death because they are trapped in a strange twilight existence called persistence. They make hardly any new proteins and grow barely, if at all. Antibiotics can’t kill persisters because there’s nothing in them to attack. The difference between normal cells and persisters cannot be found in their DNA. After persister cells survive an attack of antibiotics, some of their offspring switch back to normal growth and rebuild the colony. Most of their descendants will be normal E. coli. But some will be persisters. The colony remains the same motley crew of clones.

The key to understanding E. coli’s fingerprints is to recognize that the bacteria are not simple machines. Unlike wires and transistors, E. coli’s molecules are floppy, twitchy and unpredictable. In an electronic device, like a computer or a radio, electrons stream in a steady flow through the machine’s circuits, but the molecules in E. coli jostle and wander. When E. coli begins using a gene to make a protein, it does not produce a smoothly increasing supply. It spurts out the proteins in fits and starts. One clone may produce half a dozen copies of a protein in an hour, while a clone right next to it produces none.

Michael Elowitz, a physicist at Caltech, put these bursts on display in an elegant experiment. He and his colleagues incited E. coli to produce its proteins for feeding on lactose. Dr. Elowitz and his colleagues added extra genes to the bacteria so that when they made lactose-digesting proteins, they also released light.

The bacteria, Dr. Elowitz found, did not produce a uniform glow. They flickered, sometimes brightly, sometimes dimly. And when Dr. Elowitz took a snapshot of the colony, it was not a uniform sea of light. Some microbes were dark at that moment while others shone at full strength.

These noisy bursts can have long-term effects on how E. coli behaves. It is delicately balanced between very different states, and a little nudge can sometimes push it one way or the other.

Under some conditions, for example, it is very easy to make E. coli an eager lactose-feeder, or a reluctant one. By pure chance, a microbe may make a lot of lactose-sucking channels, causing it to draw in a lot of the sugar. Lactose can pull repressing proteins away from E. coli’s genes, causing the microbe to make more channels along with enzymes. That causes even more lactose to pour into the cell. The microbe becomes locked in a sugar-feasting feedback loop.

On the other hand, the same microbe, through pure chance, may not produce that burst of channels. It cannot pull in any extra lactose. The few lactose molecules that can seep through its membrane are too few to pull off the repressor proteins. Its lactose-digesting genes stay switched off, and it cannot enjoy a snack of milk sugar. It is trapped in its own negative feedback loop.

Other studies suggest that the unpredictable noisiness in E. coli’s cellular machinery is also responsible for persistence, hairy coats, selfless suicide and vulnerability to viruses. The big question for many scientists is why E. coli has evolved so that noise can produce such drastic changes in its biology.

Mathematical models suggest E. coli uses noise as a way to hedge its bets. A colony of E. coli can’t simply wait until they’re doused with antibiotics to slip into persistence. They’d be killed before they were done. Instead, noise causes a fraction of them to be persisters. If they do get hit with antibiotics, at least a few of them will survive. If the antibiotics never come, the majority of the bacteria can continue to grow and divide.

E. coli appears to follow a universal rule. Other microbes exploit noise, as do flies, worms and humans. Some of the light-sensitive cells in our eyes are tuned to green light, and others to red. The choice is a matter of chance. One protein may randomly switch on the green gene or the red gene, but not both.

In our noses, nerve cells can choose among hundreds of different kinds of odor receptors. Each cell picks only one, and evidence suggests that the choice is controlled by the unpredictable bursts of proteins within each neuron. It’s far more economical to let noise make the decision than to make proteins that can control hundreds of individual odor receptor genes.

Identical genes can also behave differently in our cells because some of our DNA is capped by carbon and hydrogen atoms called methyl groups. Methyl groups can control whether genes make proteins or remain silent. In humans (as well as in other organisms like E. coli), methyl groups sometimes fall off of DNA or become attached to new spots. Pure chance may be responsible for changing some methyl groups; nutrients and toxins may change others.

Identical twins may have nearly identical genes, but their methyl groups are distinctive by the time they are born and become increasingly different as the years pass. As the patterns change, people become more or less vulnerable to cancer or other diseases. This experience may be the reason why identical twins often die many years apart. They are not identical at all.

These different patterns are also one reason that clones of humans and animals can never be perfect replicas. DNA from a calico cat named Rainbow was used to create the first cloned kitten, named Cc. But Cc is not a carbon copy of Rainbow. Rainbow is white with splotches of brown, tan and gold. Cc has gray stripes. Rainbow is shy. Cc is outgoing. Rainbow is heavy, and Cc is sleek. Changes in methyl groups probably account for some of those differences. Clones may also be altered by the unique pattern of protein bursts in their cells. The very molecules that make them up turn them into individuals.

At the very least, E. coli’s individuality should be a warning to those who would put human nature down to any sort of simple genetic determinism. Living things are more than just programs run by genetic software. Even in minuscule microbes, the same genes and the same genetic network can lead to different fates.

Copyright 2008 Carl Zimmer
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