Authors: Carl Zimmer
Meselson and Stahl then ran a second version of the experiment. They moved some of the heavy-nitrogen
E. coli
into a flask where they could feed on normal nitrogen, with only fourteen neutrons apiece. The bacteria had just enough time to divide once before Meselson and Stahl tossed their DNA in the centrifuge. If Watson and Crick were right about how DNA reproduced, Meselson and Stahl knew what to expect. Inside each microbe, the heavy strands would have been pulled apart, and new strands made from light nitrogen would have been added to them. The DNA in the new generation of
E. coli
would be half heavy, half light. It should form a band halfway between where the light and heavy forms did. And that was precisely what Meselson and Stahl saw.
Watson and Crick might have built a beautiful model. But it took a beautiful experiment on
E. coli
for other scientists to believe it was also true.
A UNIVERSAL CODE
The discovery of
E. coli’
s sex life gave scientists a way to dissect a chromosome. It turned out that
E. coli
has a peculiar sort of sex, with one microbe casting out a kind of molecular grappling hook to reel in a partner. Its DNA moves into the other microbe over the course of an hour and a half. Élie Wollman and François Jacob, both at the Pasteur Institute in Paris, realized that they could break off this liaison. They mixed mutants together and let them mate for a short time before throwing them into a blender. Depending on how long the bacteria were allowed to mate, the recipient might or might not get a gene it needed to survive. By timing how long it took various genes to enter
E. coli,
Wollman and Jacob could create a genetic map. It turned out that
E. coli’
s genes are arrayed on a chromosome shaped in a circle.
Scientists also discovered that along with its main chromosome
E. coli
carries extra ringlets of DNA, called plasmids. Plasmids carry genes of their own, some of which they use to replicate themselves. Some plasmids also carry genes that allow them to move from one microbe to another.
E. coli
K-12’s grappling hooks, for example, are encoded by genes on plasmids. Once the microbes are joined, a copy of the plasmid’s DNA is exchanged, along with some of the chromosome itself.
As some scientists mapped
E. coli’
s genes, others tried to figure out how their codes are turned into proteins. At the Carnegie Institution in Washington, D.C., researchers fed
E. coli
radioactive amino acids, the building blocks of proteins. The amino acids ended up clustered around pellet-shaped structures scattered around the microbe, known as ribosomes. Loose amino acids went into the ribosomes, and full-fledged proteins came out. Somehow the instructions from
E. coli’
s DNA had to get to the ribosomes to tell them what proteins to make.
It turned out that
E. coli
makes special messenger molecules for the job. The first step in making a protein requires an enzyme to clamp on to a gene and crawl along its length. It builds a single-stranded version of the gene from RNA. This RNA can then move to a ribosome, delivering its genetic message.
How a ribosome reads that message was far from clear, though. RNA, like DNA, is made of four different bases. Proteins are combinations of twenty amino acids.
E. coli
needs some kind of dictionary to translate instructions written in the language of genes into the language of proteins.
In 1957, Francis Crick drafted what he imagined the dictionary might look like. Each amino acid was encoded by a string of three bases, known as a codon. Marshall Nirenberg and Heinrich Matthaei, two scientists at the National Institutes of Health, soon began an experiment to see if Crick’s dictionary was accurate. They ground up
E. coli
with a mortar and pestle and poured its innards into a series of test tubes. To each test tube they added a different type of amino acid. Then Nirenberg and Matthaei added the same codon to each tube: three copies of uracil (a base found in RNA but not in DNA). They waited to see if the codon would recognize one of the amino acids.
In nineteen tubes nothing happened. The twentieth tube was filled with the amino acid phenylalanine, and only in that tube did new proteins form. Nirenberg and Matthaei had discovered the first entry in life’s dictionary: UUU equals phenylalanine. Over the next few years they and other scientists would decipher
E. coli’
s entire genetic code.
Having deciphered the genetic code of a species for the first time, Nirenberg and his colleagues then compared
E. coli
to animals. They filled test tubes with the crushed cells of frogs and guinea pigs, and added codons of RNA to them. Both frogs and guinea pigs followed the same recipe for building proteins as
E. coli
had. In 1967, Nirenberg and his colleagues announced they had found “an essentially universal code.”
Nirenberg would share a Nobel Prize for Medicine the following year. Delbrück got his the year after. Lederberg, Tatum, and many others who worked on
E. coli
were also summoned to Stockholm. A humble resident of the gut had led them to glory and to a new kind of science, known as molecular biology, that unified all of life. Jacques Monod, another of
E. coli’
s Nobelists, gave Albert Kluyver’s old claim a new twist, one that many scientists still repeat today.
“What is true for
E. coli
is true for the elephant.”
THE SHAPE OF LIFE
With the birth of molecular biology, genes came to define what it means to be alive. In 2000, President Bill Clinton announced that scientists had completed a rough draft of the human genome—the entire sequence of humans’ DNA. He declared, “Today, we are learning the language in which God created life.”
But on their own, genes are dead, their instructions meaningless. If you coax the chromosome out of
E. coli,
it cannot build proteins by itself. It will not feed. It will not reproduce. The fragile loop of DNA will simply fall apart. Understanding an organism’s genes is only the first step in understanding what it means for the organism to be alive.
Many biologists have spent their careers understanding what it means for
E. coli
in particular to be alive. Rather than starting from scratch with another species, they have built on the work of earlier generations. Success has bred more success. In 1997, scientists published a map of
E. coli’
s K-12’s entire genome, including the location of 4,288 genes. The collective knowledge about
E. coli
makes it relatively simple for a scientist to create a mutant missing any one of those genes and then to learn from its behavior what that gene is for. Scientists now have a good idea of what all but about 600 genes in
E. coli
are for. From the hundreds of thousands of papers scientists have published on
E. coli
comes a portrait of a living thing governed by rules that often apply, in one form or another, to all life. When Jacques Monod boasted of
E. coli
and the elephant, he was speaking only of genes and proteins. But
E. coli
turns out to be far more complex—and far more like us—than Monod’s generation of scientists realized.
The most obvious thing one notices about
E. coli
is that one can notice
E. coli
at all. It is not a hazy cloud of molecules. It is a densely stuffed package with an inside and an outside. Life’s boundaries take many forms. Humans are wrapped in soft skin, crabs in a hard exoskeleton. Redwoods grow bark, squid a rubbery sheet.
E. coli’
s boundary is just a few hundred atoms thick, but it is by no means simple. It is actually a series of layers within layers, each with its own subtle structure and complicated jobs to carry out.
E. coli’
s outermost layer is a capsule of sugar teased like threads of cotton candy. Scientists suspect it serves to frustrate viruses trying to latch on and perhaps to ward off attacks from our immune system. Below the sugar lies a pair of membranes, one nested in the other. The membranes block big molecules from entering
E. coli
and keep the microbe’s molecules from getting out.
E. coli
depends on those molecules reacting with one another in a constant flurry. Keeping its 60 million molecules packed together lets those reactions take place quickly. Without a barrier, the molecules would wander away from one another, and
E. coli
would no longer exist.
At the same time, though, life needs a connection to the outside world. An organism must draw in new raw materials to grow, and it must flush out its poisonous waste. If it can’t, it becomes a coffin.
E. coli’
s solution is to build hundreds of thousands of pores, channels, and pumps on the outer membrane. Each opening has a shape that allows only certain molecules through. Some swing open for their particular molecule, as if by password.
Once a molecule makes its way through the outer membrane, it is only half done with its journey. Between the outer and inner membranes of
E. coli
is a thin cushion of fluid, called the periplasm. The periplasm is loaded with enzymes that can disable dangerous molecules before they are able to pass through the inner membrane. They can also break down valuable molecules so that they can fit in channels embedded in the inner membrane. Meanwhile,
E. coli
can truck its waste out through other channels. Matter flows in and out of
E. coli,
but rather than making a random, lethal surge, it flows in a selective stream.
E. coli
has a clever solution to one of the universal problems of life. Yet solutions have a way of creating problems of their own.
E. coli’
s barriers leave the microbe forever on the verge of exploding. Water molecules are small enough to slip in and out of its membranes. But there’s not much room for water molecules inside
E. coli,
thanks to all the proteins and other big molecules. So at any moment more water molecules are trying to get into the microbe than are trying to get out. The force of this incoming water creates an enormous pressure inside
E. coli,
several times higher than the pressure of the atmosphere. Even a small hole is big enough to make
E. coli
explode. If you prick us, we bleed, but if you prick
E. coli,
it blasts.
One way
E. coli
defends against its self-imposed pressure is with a corset. It creates an interlocking set of molecules that form a mesh that floats between the inner and outer membranes. The corset (known as the peptidoglycan layer) has the strength to withstand the force of the incoming water.
E. coli
also dispatches a small army of enzymes to the membranes to repair any molecules damaged by acid, radiation, or other abuse. In order to grow, it must continually rebuild its membranes and peptidoglycan layer, carefully inserting new molecules without ever leaving a gap for even a moment.
E. coli’
s quandary is one we face as well. Our own cells carefully regulate the flow of matter through their walls. Our bodies use skin as a barrier, which must also be pierced with holes—for sweat glands, ear canals, and so on. Damaged old skin cells slough off as the underlying ones grow and divide. So do the cells of the lining of our digestive tract, which is essentially just an interior skin. This quick turnover allows our barriers to heal quickly and fend off infection. But it also creates its own danger. Each time a cell divides, it runs a small risk of mutating and turning cancerous. It’s not surprising, then, that skin cancer and colon cancer are among the most common forms of the disease. Humans and
E. coli
alike must pay a price to avoid becoming a blur.
THE RIVER THAT RUNS UPHILL
Barriers and genes are essential to life, but life cannot survive with barriers and genes alone. Put DNA in a membrane, and you create nothing more than a dead bubble. Life also needs a way to draw in molecules and energy, to transform them into more of itself. It needs a metabolism.
Metabolisms are made up of hundreds of chemical reactions. Each reaction may be relatively simple: an enzyme may do nothing more than pull a hydrogen atom off a molecule, for instance. But that molecule is then ready to be grabbed by another enzyme that will rework it in another way, and so on through a chain of reactions that can become hideously intricate—merging with other chains, branching in two, or looping back in a circle. The first species whose metabolism scientists mapped in fine detail was
E. coli.
It took them the better part of the twentieth century. To uncover its pathways, they manipulated it in many ways, such as feeding it radioactive food so that they could trace atoms as
E. coli
passed them from molecule to molecule. It was slow, tough, unglamorous work. After James Watson and Francis Crick discovered the structure of DNA, their photograph appeared in
Life
magazine: two scientists flanking a tall, bare sculpture. There was no picture of the scientists who collectively mapped
E. coli’
s metabolism. It would have been a bad photograph anyway: hundreds of people packed around a diagram crisscrossed with so many arrows that it looked vaguely like a cat’s hairball. But for those who know how to read that diagram,
E. coli’
s metabolism has a hidden elegance.
The chemical reactions that make up
E. coli’
s metabolism don’t happen spontaneously, just as an egg does not boil itself. It takes energy to join atoms together, as well as to break them apart.
E. coli
gets its energy in two ways. One is by turning its membranes into a battery. The other is by capturing the energy in its food.
Among the channels that decorate
E. coli’
s membranes are pumps that hurl positively charged protons out of the microbe.
E. coli
gives itself a negative charge in the process, attracting positively charged atoms that happen to be in its neighborhood. It draws some of them into special channels that can capture energy from their movement, like an electric version of a waterwheel.
E. coli
stores that energy in the atomic bonds of a molecule called adenosine triphosphate, or ATP.