Microcosm

by Carl Zimmer

  The bow tie architecture in E. coli makes good engineering sense. Man-made networks, such as a telephone network or a power grid, are often laid out in a bow tie as well. A bow tie architecture lets networks run efficiently and robustly. The Internet, for example, has an incoming fan made up of signals from e-mail programs, Web browsers, and all sorts of other software, each with its own peculiar sorts of information processing. In order for this stream of data to get onto the Internet, it must first be turned into a code that obeys the Internet’s protocols. These data streams move from personal computers to servers and then into a small core of routers. The signals can then flow into an outgoing fan of pathways, toward another computer, where the standard stream of data can be converted into a picture, a document, or some other peculiar form.

  In both the Internet and E. coli, the bow tie knot allows each network to function even when parts of it fail. A mutation that destroys one metabolic reaction will not kill E. coli because in the knot there are other pathways onto which it can still shunt carbon. The Internet can continue sending messages even after one of the servers shuts down because it can move the messages through another pathway.

  The bow tie architecture also saves energy in both systems. If E. coli did not have a bow tie, it would have to create a dedicated pathway of enzymes to make every molecule it needed. Each of those enzymes would require its own gene. Instead, E. coli’s pathways all dump their products into the same network in the knot of the bow tie. Likewise, the Internet does not have to link every computer directly to every other one, or use special codes for every kind of file it carries. In both cases this arrangement is possible only because the entire network obeys certain rules. On the Internet every message must be converted into the same data packets. In E. coli all energy transfers must use the same currency: ATP.

  The inventors of the Internet did not realize they were creating this kind of network. They were only trying to balance cost and speed as they joined servers together. But unintentionally they created a model of E. coli that spans the Earth.

  VIVE LA DIFFÉRENCE

  We all have our own tastes. I don’t understand why some people eat snails. I can’t say for sure why I dislike them, but I can certainly think up a few stories. Maybe I have a certain kind of sensor on the cells of my tongue that goes into a spasm of dismay. Or maybe some network of neurons in my brain associates the taste of snails with some awful memory from my distant past. Or maybe I simply never had the opportunity to come to love snails because I grew up eating pizza and hamburgers and peanut butter. The gastronomic window has now closed.

  I have no way of knowing whether any of those possibilities is true. I can’t go back in time, replay my life from the moment of conception, and see if a plate of escargots served at kindergarten lunch would have made a difference. I can’t clone myself a hundred times over and send my manufactured twins to foster homes in France. I am a single, useless snail-loathing datum.

  My distaste for snails is a minor example of a major fact: life is full of differences. We humans differ from one another in ways too many to count. We are shy and bold, freckled and pale, truckers and hairdressers, Buddhists and Presbyterians. We get cancers in third grade and live for a century. We have fingerprints.

  Scientists have only a rough understanding of how this diversity arises. We are not merely the output of software written in a programming code of DNA. As we develop in the womb, our genes interact with signals from our mothers. The environment continues to influence those genes in unpredictable ways after birth. The food we eat, the air we breathe, the traumas and joys and boredom of childhood, and all the rest have an influence on which genes become active. Our differences are not just hard to trace but a source of pride. We can produce greatness of all kinds: Babe Ruths and Frédéric Chopins, Mae Wests and Marie Curies. They are products of our complexity, of a species in which each individual carries 18,000 genes that can become 100,000 proteins, which give rise to creatures uniquely able to experience the world, to shape their lives by words, rituals, images. And this pride colors our image of E. coli.

  Surely E. coli must be all nature and no nurture. A colony descended from a single ancestor is just a billion genetically identical cousins, their behavior all run through the same genetic circuits. E. coli is just a single cell, after all, not a body made of a trillion cells that take years to develop. E. coli doesn’t grow up going to private school or searching for food on a garbage dump. It doesn’t wonder whether it might like snails for dinner. It’s just a bag of molecules. If it is genetically identical to another E. coli, then the two of them will live identical lives.

  This may all sound plausible, but it is 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 you observe two genetically identical E. coli swimming side by side, for example, one may give up while the other keeps spinning its flagella. To gauge their stamina, Daniel Koshland, a scientist at the University of California, Berkeley, glued genetically identical E. coli to a glass cover slip. They floated in water, tethered by their flagella. Koshland offered them a taste of aspartate, an amino acid that attracts them and motivates them to swim. Stuck to the slide, the bacteria could only pirouette. Koshland found that some of the clones twirled twice as long as others.

  E. coli expresses its individuality in other ways. In a colony of genetically identical clones, some will produce sticky hairs on their surface, and some will not. In a rapidly breeding colony, a few individual microbes will stop growing, entering a peculiar state of suspended animation. In a colony of E. coli, some clones like milk sugar, and others don’t.

  These differing tastes for lactose first came to light in 1957. Aaron Novick and Milton Weiner, two biologists at the University of Chicago, looked at how individual E. coli, respond to the presence of lactose. They fed E. coli a lactoselike molecule that could also trigger the bacteria to make beta-galactosidase. At low levels only a tiny fraction of the microbes responded by producing beta-galactosidase. Most did nothing.

  Novick and Weiner added more of the lactose mimic. The eager individuals remained eager. The reluctant ones remained reluctant. Only after the lactose mimic rose above a threshold did the reluctant microbes change. Suddenly they produced beta-galactosidase as quickly as the eager microbes.

  Somehow the bacteria were behaving in radically different ways even though they were all genetically identical. Novick and Weiner isolated eager and reluctant individuals and transferred them to fresh petri dishes, where they could breed new colonies of their own. Their descendants continued to behave in the same way. Eager begat eager; reluctant, reluctant. Novick and Weiner had found a legacy beyond heredity.

  There’s much to be learned about E. coli by thinking of it as a machine with circuitry that follows the fundamental rules of engineering. But only up to a point. Two Boeing 777s that are in equally good working order should behave in precisely the same way. Yet if they were like E. coli, one might turn south when the other turned north.

  The difference between E. coli and the planes lies in the stuff from which they are made. Unlike wires and transistors, E. coli’s molecules are floppy, twitchy, and unpredictable. They work in fits and starts. In a plane, electrons stream in a steady flow through its circuits, but the molecules in E. coli jostle and wander. When a gene switches on, E. coli does not produce a smoothly increasing supply of the corresponding protein. A single E. coli spurts out its proteins unpredictably. If its lac operon turns on, it may spit out six beta-galactosidase enzymes in the first hour, or none at all.

  This burstiness helps turn genetically identical E. coli into a crowd of individuals. Michael Elowitz, a physicist at Cal Tech, made E. coli’s individuality visible in an elegant experiment. He and his colleagues added an extra gene to the lac operon, encoding a protein that gave off light. When he triggered the bacteria to turn on the operon, they began to mak
e the glowing proteins. But instead of glowing steadily, they flickered. Each burst of fluorescent proteins gave off a pulse of light. Some bursts were big, and some were small. And when 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 produce long-term differences between genetically identical bacteria. They turn out to be responsible for making some E. coli eager for lactose and others reluctant. If you could peer inside a reluctant E. coli, you would find a repressor clamped tightly to the lac operon. Lactose can sometimes seep through the microbe’s membrane, and it can even sometimes pry away the repressor. Once the lac operon is exposed, E. coli’s gene-reading enzymes can get to work very quickly. They make an RNA copy of the operon’s genes, which is taken up by a ribosome and turned into proteins, including a beta-galactosidase enzyme.

  But each E. coli usually contains about three repressors. They spend most of their time sliding up and down the microbe’s DNA, searching for the lac operon. It takes only a few minutes for one of them to find it and shut down the production of beta-galactosidase. Only a tiny amount of beta-galactosidase gets made in those brief moments of liberty. And what few enzymes do get made are soon ripped apart by E. coli’s army of protein destroyers. Adding a little more lactose does not change the state of affairs. Too little of the sugar gets into the microbe to keep the repressors away from the lac operon for long. The microbe remains reluctant.

  Keep increasing the lactose, however, and this reluctant microbe will suddenly turn eager. There’s a threshold beyond which it produces lots of beta-galactosidase. The secret to this reversal is one of the other genes in the lac operon. Along with beta-galactosidase, E. coli makes the protein permease, which sucks lactose molecules into the microbe. When a reluctant E. coli’s lac operon switches on briefly, some of these permeases get produced. They begin pumping more lactose into the microbe, and that extra lactose can pull away more repressors. The lac operon can turn on for longer periods before a repressor can shut it down again, and so it makes more proteins—both beta-galactosidase for digesting lactose and permease for pumping in more lactose. A positive feedback sets in: more permease leads to more lactose, which leads to more permease, which leads to more lactose. The feedback drives E. coli into a new state, in which it produces beta-galactosidase and digests lactose as fast as it can.

  Once it becomes eager, E. coli will resist changing back. If the concentration of lactose drops, the microbe will still pump in lactose at a high rate, thanks to all the permease channels it has built. It can supply itself with enough lactose to keep the repressors away from the operon so that it can continue making beta-galactosidase and permease. Only if the lactose concentrations drop below a critical level do the repressors suddenly get the upper hand. Then they shut the operon down, and the microbe turns off.

  This sticky switch helps to make sense of Novick and Weiner’s strange experiments. Two genetically identical E. coli can respond differently to the same level of lactose because they have different histories. The reluctant one resists being switched on while the eager one resists being switched off. And both kinds can pass on their state to their offspring. They don’t bequeath different genes to their descendants. Some give their offspring a lot of permeases on their membranes and a lot of lactose molecules floating through their interiors. Others give their offspring neither.

  Combine this peculiar switch with E. coli’s unpredictable bursts and you have a recipe for individuality. If a colony of E. coli encounters some lactose, some of the bacteria will respond with a huge burst of proteins from their lac operon. They will push themselves over the threshold from reluctant to eager, and they will stay that way even if the lactose drops. Other E. coli will respond to the lactose with no proteins at all. They will remain reluctant. These clones take on different personalities thanks to chance alone.

  E. coli also gets some of its personality from an extra layer of heredity. Some of its DNA is covered with caps made of hydrogen and carbon atoms. These caps, known as methyl groups, change the response of E. coli’s genes to incoming signals. They can, in effect, shut a gene down for a microbe’s entire life without harming the gene itself. When E. coli divides in two, it bequeaths its pattern of methyl groups to its offspring. But under certain conditions, E. coli will pull methyl groups off its DNA and put new groups on—for reasons scientists don’t yet understand.

  Some of the factors that spin the wheel for E. coli spin it for us as well. To smell, for example, we depend on hundreds of different receptors on the nerve endings in our noses. Each neuron makes only one type of receptor. Which receptor it makes seems to be a matter of chance, determined by the unpredictable bursts of proteins within each neuron. Our DNA carries methyl groups as well, and over our lifetime their pattern can change. Pure chance may be responsible for some changes; nutrients and toxins may trigger others. Identical twins may have 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 after all.

  These different patterns are also one reason why clones of humans and animals can never be perfect replicas. In 2002, scientists in Texas reported that they had used DNA from a calico cat named Rainbow to create the first cloned kitten, which they 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. New methylation patterns probably account for some of those differences. Clones may also get hit by a unique series of protein bursts. The very molecules that make them up turn them into individuals in their own right.

  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.

  Four

  THE E. COLI WATCHER’S FIELD GUIDE

  A HUMAN KRAKATAU

  ON AUGUST 26, 1883, a little world was born. An island volcano called Krakatau, located between Java and Sumatra in the Sunda Strait, hurled a column of ash twenty miles into the air. Rock turned to vapor and roared across the strait at 300 miles an hour. The eruption left a submerged pit where the cone of the volcano had been, along with a few lifeless islands. Nine months later, a naturalist who visited the scene reported that the only living thing he could find was a single small spider.

  The new islands of Krakatau lay twenty-seven miles from the nearest land. It took years for life to make its way across the water and take hold again. A film of blue-green algae grew over the ash. Ferns and mosses sprouted. By the 1890s a savanna had emerged. Along with the spiders came beetles, butterflies, and even a monitor lizard. Some of the arriving species swam to the islands, some flew, and some simply drifted on the wind.

  These species did not take hold on Krakatau in a random scramble. Rugged pioneers came first and later gave way to other species. The savanna surrendered to forests. Coconut and fig trees grew. Orchids, fig wasps, and other delicate species could now move onto the islands. Early settlers such as zebra doves could no longer find a place in the food web and vanished. Even now, more than 120 years after the eruption, Krakatau is not finished with its transformation. In the future it may be ready to receive bamboo, which will revolutionize its ecosystem yet again.

  The history of Krakatau followed ecological rules that guide life wherever new habitats appear. Volcanic eruptions wipe islands clean. Landslides clear mountainsides. As glaciers melt, shorelines bounce out of the sea.

  And babies are born. To microbes, a newborn child is a Krakatau ready to be colonized. Its body starts out almost completely germ free,
and in its first few days E. coli and other species of bacteria infect it. They establish a new ecosystem, which will mature and survive within the child through its entire life. And it will develop over time according to its own ecological rules.

  There is much more to E. coli’s life than can be seen in a petri dish. Its pampered existence in the laboratory makes very few demands on it. Out of the 4,288 genes scientists have identified in E. coli K-12, only 303 appear to be essential for its growth in a laboratory. That does not mean the other 3,985 genes are all useless. Many help E. coli survive in the crowded ecosystem of the human gut, where a thousand species of microbes compete for food.

  A scientist studying E. coli in a flask may completely overlook some of its essential strategies for surviving in the real world. For all the work that has gone into E. coli over the past century, for example, microbiologists often fail to acknowledge just how social a creature it is. To survive, E. coli work together. The bacteria communicate and cooperate. Billions of them join together to build microbial cities. They wage wars together against their enemies.

  In the real world there is no single way of being an E. coli. E. coli K-12 is just one of many strains that live in warm-blooded animals and have many strategies for surviving. Some are harmless gut grazers. Others shield us from infections. And still others kill millions of people a year. To know E. coli by K-12 alone is a bit like knowing the family Canidae from a Pomeranian dozing on a silk pillow. Outside there are dingoes and bat-eared foxes, red wolves and black-backed jackals.

  FINDING A HOME

  E. coli is a pioneer. Long before most other microbes have moved into a human host, it has established a healthy colony. E. coli may infect a baby during the messy business of childbirth, hitch along on the fingertips of a doctor, or make its leap as mother nurses child. It rides waves of peristalsis into the stomach, where it must survive an acid bath. As the swarms of protons in hydrochloric acid seep into it, E. coli builds extra pumps that can flush most of them out. It does not try to behave like a normal microbe in the stomach; instead, it enters what one scientist has called “a Zen-like physiology.” Except for the proteins it needs to defend against stomach acid, E. coli simply stops making proteins altogether.