Microcosm (4 page)

ATP molecules float through
E. coli
like portable energy packs. When
E. coli’
s enzymes need extra energy to drive a reaction, they grab ATP and draw out the energy stored in the bonds between its atoms.
E. coli
uses the energy it gets from its membrane battery to get more energy from its food. With the help of ATP, its enzymes can break down sugar, cutting its bonds and storing the energy in still more ATP. It does not unleash all the energy in a sugar molecule at once. If it did, most of that energy would be lost in heat. Rather than burning up a bonfire of sugar,
E. coli
makes surgical nicks, step by step, in order to release manageable bursts of energy.

E. coli
uses some of this energy to build new molecules. Along with the sugar it breaks down, it also needs a few minerals. But it has to work hard to get even the trace amounts it requires.
E. coli
needs iron to live, for example, but iron is exquisitely scarce. In a living host most iron is tucked away inside cells. What little there is outside the cells is usually bound up in other molecules, which will not surrender it easily.
E. coli
has to fight for iron by building iron-stealing molecules, called siderophores, and pumping them out into its surroundings. As the siderophores drift along, they sometimes bump into iron-bearing molecules. When they do, they pry away the iron atom and then slide back into
E. coli.
Once inside, the siderophores unfold to release their treasure.

While iron is essential to
E. coli,
it’s also a poison. Once inside the microbe, a free iron atom can seize oxygen atoms from water molecules, turning them into hydrogen peroxide, which in turn will attack
E. coli’
s DNA.
E. coli
defends itself with proteins that scoop up iron as soon as it arrives and store it away in deep pockets. A single one of these proteins can safely hold 5,000 iron atoms, which it carefully dispenses, one atom at a time, as the microbe needs them.

Iron is not the only danger
E. coli’
s metabolism poses to itself. Even the proteins it builds can become poisonous. Acid, radiation, and other sorts of damage can deform proteins, causing them to stop working as they should. The mangled proteins wreak havoc, jamming the smooth assembly line of chemistry
E. coli
depends on for survival. They can even attack other proteins.
E. coli
protects itself from itself by building a team of assassins—proteins whose sole function is to destroy old proteins. Once an old protein has been minced into amino acids, it becomes a supply of raw ingredients for new proteins. Life and death, food and poison—all teeter together on a delicate fulcrum inside
E. coli
.

As
E. coli
juggles iron, captures energy, and transforms sugar into complex molecules, it seems to defy the universe. There’s a powerful drive throughout the universe, known as entropy, that pushes order toward disorder. Elegant snowflakes melt into drops of water. Teacups shatter.
E. coli
seems to push against the universe, assembling atoms into intricate proteins and genes and preserving that orderliness from one generation to the next. It’s like a river that flows uphill.

E. coli
is not really so defiant. It is not sealed off from the rest of the universe. It does indeed reduce its own entropy, but only by consuming energy it gets from outside. And while
E. coli
increases its own internal order, it adds to the entropy of the universe with its heat and waste. On balance,
E. coli
actually increases entropy, but it manages to bob on the rising tide.

E. coli’
s metabolism is something of a microcosm of life as a whole. Most living things ultimately get their energy from the sun. Plants and photosynthetic microbes capture light and use its energy to grow. Other species eat the photosynthesizers, and still other species eat them in turn.
E. coli
sits relatively high up in this food web, feeding on the sugars made by mammals and birds. It gets eaten in turn, its molecules transformed into predatory bacteria or viruses, which get eaten as well. This flow of energy gives rise to forests and other ecosystems, all of which unload their entropy on the rest of the universe. Sunlight strikes the planet, heat rises from it, and a planet full of life—an
E. coli
for the Earth—sustains itself on the flow.

A SENSE OF WHERE YOU ARE

Life’s list grows longer. It stores information in genes. It needs barriers to stay alive. It captures energy and food to build new living matter. But if life cannot find that food, it will not survive for long. Living things need to move—to fly, squirm, drift, send tendrils up gutter spouts. And to make sure they’re going in the right direction, most living things have to decide where to go.

We humans use 100 billion neurons bundled in our heads to make that decision. Our senses funnel rivers of information to the brain, and it responds with signals that control the movements of our bodies.
E. coli,
on the other hand, has no brain. It has no nervous system. It is, in fact, thousands of times smaller than a single human nerve cell. And yet it is not oblivious to its world. It can harvest information and manufacture decisions, such as where it should go next.

E. coli
swims like a spastic submarine. Along the sides of its cigar-shaped body it sprouts about half a dozen propellers. They’re shaped like whips, trailing far behind the microbe. Each tail (or, as microbiologists call it, flagellum) has a flexible hook at its base, which is anchored to a motor. The motor, a wheel-shaped cluster of proteins, can spin 250 times a second, powered by protons that flow through its pores into the microbe’s interior.

Most of the time,
E. coli’
s motors turn counterclockwise, and when they do their flagella all bundle together into a cable. They behave so neatly because each flagellum is slightly twisted in the same direction, like the ribbons on a barber’s pole. The cable of flagella spin together, pushing against the surrounding fluid in the process, driving the microbe forward.

E. coli
can swim ten times its body length in a second. The fastest human swimmers can move only two body lengths in that time. And
E. coli
wins this race with a handicap, because the physics of water is different for microbes than for large animals like us. For
E. coli,
water is as viscous as mineral oil. When it stops swimming, it comes to a halt in a millionth of a second.
E. coli
does not stop on a dime. It stops on an atom.

About every second or so,
E. coli
throws its motors in reverse and hurls itself into a tumble. When its motors spin clockwise, the flagella can no longer slide comfortably over one another. Now their twists cause them to push apart; their neat braid flies out in all directions. It now looks more like a fright wig than a barber’s pole. The tumble lasts only a tenth of a second as
E. coli
turns its motors counterclockwise once more. The flagella fold together again, and the microbe swims off.

The first scientist to get a good look at how
E. coli
swims was Howard Berg, a Harvard biophysicist. In the early 1970s, Berg built a microscope that could follow a single
E. coli
as it traveled around a drop of water. Each tumble left
E. coli
pointing in a new random direction. Berg drew a single microbe’s path over the course of a few minutes and ended up with a tangle, like a ball of yarn in zero gravity. For all its busy swimming, Berg found,
E. coli
manages to wander only within a tiny space, getting nowhere fast.

E. coli’
s flagellum is driven by motorlike proteins that spin in its membrane.

Offer
E. coli
a taste of something interesting, however, and it will give chase.
E. coli’
s ability to navigate is remarkable when you consider how little it has to work with. It cannot wheel and bank a pair of wings. All it can do is swim in a straight line or tumble. And it can get very little information about its surroundings. It cannot consult an atlas. It can only sense the molecules it happens to bump into in its wanderings. But
E. coli
makes good use of what little it has. With a few elegant rules, it gets where it needs to go.

E. coli
builds sensors and inserts them in its membranes so that their outer ends reach up like periscopes. Several thousand sensors cluster together at the microbe’s front tip, where they act like a microbial tongue. They come in five types, each able to grab certain kinds of molecules. Some types attract
E. coli,
and some repel it. An attractive molecule, such as the amino acid serine, sets in motion a series of chemical reactions inside the microbe with a simple result:
E. coli
swims longer between its tumbles. It will keep swimming in longer runs as long as it senses that the concentration of serine is rising. If its tumbles send it away from the source of serine, its swims become shorter. This bias is enough to direct
E. coli
slowly but reliably toward the serine. Once it gets to the source, it stays there by switching back to its aimless wandering.

Scientists began piecing together
E. coli’
s system of sensing and swimming in the 1960s. They chose
E. coli’
s system because they thought it would be easy. They could take advantage of the long tradition of using mutant
E. coli
to study how proteins work. And once they had solved
E. coli’
s information processors, they would be able to take what they had learned and apply it to more complex processors, including our own brains. Forty years later they understand
E. coli’
s signaling system more thoroughly than that of any other species. Some parts of
E. coli’
s system turned out to be simple after all.
E. coli
does not have to compute barrel rolls or spiral dives. Its swim-and-tumble strategy works very well. Every
E. coli
may not get exactly where it needs to go, but many of them will. They will be able to survive and reproduce and pass the run-and-tumble strategy on to their offspring. That is all the success a microbe needs.

Yet in some important ways,
E. coli’
s navigation defies understanding. Its microbial tongue can detect astonishingly tiny changes in the concentration of molecules it cares about, down to one part in a thousand. The microbe is able to amplify these faint signals in a way that scientists have not yet discovered. It’s possible that
E. coli’
s receptors are working together. As one receptor twists, it causes neighboring receptors to twist as well.
E. coli
may even be able to integrate different kinds of information at the same time—oxygen climbing, nickel falling, glucose wafting by. Its array of receptors may turn out to be far more than just a microbial tongue. It may be more like a brain.

THE MYTH OF THE TANGLED SPAGHETTI

E. coli’
s brainy tongue does not fit well into the traditional picture of bacteria as primitive, simple creatures. Well into the twentieth century, bacteria remained saddled with a reputation as relics of life’s earliest stages. They were supposedly nothing more than bags of enzymes with some loose DNA tossed in like a bowl of tangled spaghetti. “Higher” organisms, on the other hand—including animals, plants, fungi—were seen as having marvelously organized cells. They all keep their DNA neatly wound up around spool-shaped proteins and bundled together into chromosomes. The chromosomes are tucked into a nucleus. The cells have other compartments, in which they carry out other jobs, such as generating energy or putting the finishing touches on proteins. The cells themselves have structure, thanks to a skeletal network of fibers crisscrossing their girth.

The contrast between these two kinds of cells—sloppy and neat—seemed so stark in the mid-1900s that scientists used it to divide all of life into two great groups. All species that carried a nucleus were eukaryotes, meaning “true kernels” in Greek. All other species—including
E. coli
—were now prokaryotes. Before the kernel there were prokaryotes, primitive and disorganized. Only later did eukaryotes evolve, bringing order to the world.

There’s a kernel of truth to this story. The last common ancestor of all living things almost certainly didn’t have a nucleus. It probably looked vaguely like today’s prokaryotes. Eukaryotes split off from prokaryotes more than 3 billion years ago, and only later did they acquire a full-fledged nucleus and other distinctive features. But it is all too easy to see more differences between prokaryotes and eukaryotes than actually exist. The organization of eukaryotes jumps out at the eye. It is easy to see the chromosomes in a human cell, the intricately folded Golgi apparatus, the sausage-shaped mitochondria. The geography is obvious. But prokaryotes, it turns out, have a geography as well. They keep their molecules carefully organized, but scientists have only recently begun to discover the keys to that order.