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On a November evening last year, Jennifer Doudna put
on a stylish black evening gown and headed to Hangar One, a
building at NASA’s Ames Research Center that was constructed in
1932 to house dirigibles.

Under the looming arches of the hangar, Doudna mingled with
celebrities like Benedict Cumberbatch, Cameron Diaz and Jon Hamm
before receiving the 2015 Breakthrough Prize in life sciences, an
award sponsored by Mark Zuckerberg and other tech billionaires.

Doudna, a biochemist at the University of California, Berkeley,
and her collaborator, Emmanuelle Charpentier of the Helmholtz Centre
for Infection Research in Germany, each received $3 million for
their invention of a potentially revolutionary tool for
editing DNA known as CRISPR.

Doudna was not a gray-haired emerita being celebrated for work
she did back when dirigibles ruled the sky.

It was only in 2012 that Doudna, Charpentier and their colleagues
offered the first demonstration of CRISPR’s potential.

They crafted molecules that could enter a microbe and precisely
snip its DNA at a location of the researchers’ choosing.

In January 2013, the scientists went one step further: They cut
out a particular piece of DNA in human cells and replaced it with
another one.

In the same month, separate teams of scientists at Harvard
University and the Broad Institute reported similar success with
the gene-editing tool.

A scientific stampede commenced, and in just the past two years,
researchers have performed hundreds of experiments on CRISPR.
Their results hint that the technique may fundamentally change
both medicine and agriculture.

Some scientists have repaired defective DNA in mice, for example,
curing them of genetic disorders. Plant scientists have used
CRISPR to edit genes in crops, raising hopes that they can
engineer a better food supply.

Some researchers are trying to rewrite the genomes of elephants,
with the ultimate goal of re-creating a woolly mammoth.

Writing last year in the journal Reproductive Biology and
Endocrinology, Motoko Araki and Tetsuya Ishii of Hokkaido
University in Japan predicted that doctors will be able to use CRISPR
to alter the genes of human embryos “in the immediate future.”

Thanks to the speed of CRISPR research, the accolades have come
quickly. Last year MIT Technology Review called CRISPR “the
biggest biotech discovery of the century.”

The Breakthrough Prize is just one of several prominent awards
Doudna has won in recent months for her work on CRISPR; National
Public Radio recently reported whispers of a possible Nobel in her future.

Even the pharmaceutical industry, which is often slow to embrace
new scientific advances, is rushing to get in on the act. New
companies developing CRISPR-based medicine are opening their
doors.

In January, the pharmaceutical giant Novartis announced that it
would be using Doudna’s CRISPR technology for its research into
cancer treatments. It plans to edit the genes of immune cells so
that they will attack tumors.

But amid all the black-tie galas and patent filings, it’s easy to
overlook the most important fact about CRISPR: Nobody actually
invented it.

Doudna and other researchers did not pluck the molecules they use
for gene editing from thin air. In fact, they stumbled across the
CRISPR molecules in nature.

Microbes have been using them to edit their own DNA for millions
of years, and today they continue to do so all over the planet,
from the bottom of the sea to the recesses of our own bodies.

We’ve barely begun to understand how CRISPR works in the natural
world.

Microbes use it as a sophisticated immune system, allowing them
to learn to recognize their enemies. Now scientists are
discovering that microbes use CRISPR for other jobs as well.

The natural history of CRISPR poses many questions to scientists,
for which they don’t have very good answers yet.

Steve
Jennings/Getty Images

But it also holds great promise. Doudna and her colleagues
harnessed one type of CRISPR, but scientists are finding a vast
menagerie of different types.

Tapping that diversity could lead to more effective gene editing
technology, or open the way to applications no one has thought of
yet.

“You can imagine that many labs — including our own — are busily
looking at other variants and how they work,” Doudna said. “So
stay tuned.”

A Repeat Mystery

The scientists who discovered CRISPR had no way of knowing that
they had discovered something so revolutionary. They didn’t even
understand what they had found. In 1987, Yoshizumi Ishino and colleagues at Osaka
University in Japan published the sequence of a gene called iap
belonging to the gut microbe E. coli.

To better understand how the gene worked, the scientists also
sequenced some of the DNA surrounding it. They hoped to find
spots where proteins landed, turning iap on and off. But instead
of a switch, the scientists found something incomprehensible.

If you’ve eaten yogurt or cheese, chances are you’ve eaten
CRISPR-ized cells.

Near the iap gene lay five identical segments of DNA. DNA is made
up of building blocks called bases, and the five segments were
each composed of the same 29 bases.

These repeat sequences were separated from each other by 32-base
blocks of DNA, called spacers. Unlike the repeat sequences, each
of the spacers had a unique sequence.

This peculiar genetic sandwich didn’t look like anything
biologists had found before. When the Japanese researchers
published their results, they could only shrug. “The biological
significance of these sequences is not known,” they wrote.

It was hard to know at the time if the sequences were unique to
E. coli, because microbiologists only had crude techniques for
deciphering DNA.

But in the 1990s, technological advances allowed them to speed up
their sequencing. By the end of the decade, microbiologists could
scoop up seawater or soil and quickly sequence much of the DNA in
the sample.

This technique — called metagenomics — revealed those strange
genetic sandwiches in a staggering number of species of microbes.
They became so common that scientists needed a name to talk about
them, even if they still didn’t know what the sequences were for.

In 2002, Ruud Jansen of Utrecht University in the Netherlands and
colleagues dubbed these sandwiches “clustered regularly
interspaced short palindromic repeats” — CRISPR for short.

Jansen’s team noticed something else about CRISPR sequences: They
were always accompanied by a collection of genes nearby. They
called these genes Cas genes, for CRISPR-associated genes. The
genes encoded enzymes that could cut DNA, but no one could say
why they did so, or why they always sat next to the CRISPR
sequence.

Three years later, three teams of scientists independently
noticed something odd about CRISPR spacers. They looked a lot
like the DNA of viruses.

“And then the whole thing clicked,” said Eugene Koonin.

At the time, Koonin, an evolutionary biologist at the National
Center for Biotechnology Information in Bethesda, Md., had been
puzzling over CRISPR and Cas genes for a few years. As soon as he
learned of the discovery of bits of virus DNA in CRISPR spacers,
he realized that microbes were using CRISPR as a weapon against
viruses.

Koonin knew that microbes are not passive victims of virus
attacks. They have several lines of defense. Koonin thought that
CRISPR and Cas enzymes provide one more. In Koonin’s hypothesis,
bacteria use Cas enzymes to grab fragments of viral DNA.

They then insert the virus fragments into their own CRISPR
sequences. Later, when another virus comes along, the bacteria
can use the CRISPR sequence as a cheat sheet to recognize the
invader.

Scientists didn’t know enough about the function of CRISPR and
Cas enzymes for Koonin to make a detailed hypothesis. But his
thinking was provocative enough for a microbiologist named
Rodolphe Barrangou to test it.

To Barrangou, Koonin’s idea was not just fascinating, but
potentially a huge deal for his employer at the time, the yogurt
maker Danisco.

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Danisco depended on bacteria to convert milk into yogurt, and
sometimes entire cultures would be lost to outbreaks of
bacteria-killing viruses. Now Koonin was suggesting that bacteria
could use CRISPR as a weapon against these enemies.

To test Koonin’s hypothesis, Barrangou and his colleagues
infected the milk-fermenting microbe Streptococcus thermophilus
with two strains of viruses.

The viruses killed many of the bacteria, but some survived. When
those resistant bacteria multiplied, their descendants turned out
to be resistant too. Some genetic change had occurred.

Barrangou and his colleagues found that the bacteria had stuffed
DNA fragments from the two viruses into their spacers. When the
scientists chopped out the new spacers, the bacteria lost their
resistance.

Barrangou, now an associate professor at North Carolina State
University, said that this discovery led many manufacturers to
select for customized CRISPR sequences in their cultures, so that
the bacteria could withstand virus outbreaks. “If you’ve eaten
yogurt or cheese, chances are you’ve eaten CRISPR-ized cells,” he
said.

Cut and Paste

As CRISPR started to give up its secrets, Doudna got curious. She
had already made a name for herself as an expert on RNA, a
single-stranded cousin to DNA.

Originally, scientists had seen RNA’s main job as a messenger.
Cells would make a copy of a gene using RNA, and then use that
messenger RNA as a template for building a protein. But Doudna
and other scientists illuminated many other jobs that RNA can do,
such as acting as sensors or controlling the activity of genes.

In 2007, Blake Wiedenheft joined Doudna’s lab as a
postdoctoral researcher, eager to study the structure of Cas
enzymes to understand how they worked.

Doudna agreed to the plan — not because she thought CRISPR had
any practical value, but just because she thought the chemistry
might be cool. “You’re not trying to get to a particular goal,
except understanding,” she said.

As Wiedenheft, Doudna and their colleagues figured out the
structure of Cas enzymes, they began to see how the molecules
worked together as a system. When a virus invades a microbe, the
host cell grabs a little of the virus’s genetic material, cuts
open its own DNA, and inserts the piece of virus DNA into a
spacer.

As the CRISPR region fills with virus DNA, it becomes a molecular
most-wanted gallery, representing the enemies the microbe has
encountered. The microbe can then use this viral DNA to turn Cas
enzymes into precision-guided weapons.

The microbe copies the genetic material in each spacer into an
RNA molecule. Cas enzymes then take up one of the RNA molecules
and cradle it.

Together, the viral RNA and the Cas enzymes drift through the
cell. If they encounter genetic material from a virus that
matches the CRISPR RNA, the RNA latches on tightly. The Cas
enzymes then chop the DNA in two, preventing the virus from
replicating.

As CRISPR’s biology emerged, it began to make other microbial
defenses look downright primitive. Using CRISPR, microbes could,
in effect, program their enzymes to seek out any short sequence
of DNA and attack it exclusively.

“Once we understood it as a programmable DNA-cutting enzyme,
there was an interesting transition,” Doudna said. She and her
colleagues realized there might be a very practical use for
CRISPR. Doudna recalls thinking, “Oh my gosh, this could be a
tool.”

It wasn’t the first time a scientist had borrowed a trick from
microbes to build a tool. Some microbes defend themselves from
invasion by using molecules known as restriction enzymes. The
enzymes chop up any DNA that isn’t protected by molecular
shields.

The microbes shield their own genes, and then attack the naked
DNA of viruses and other parasites. In the 1970s, molecular
biologists figured out how to use restriction enzymes to cut DNA,
giving birth to the modern biotechnology industry.

In the decades that followed, genetic engineering improved
tremendously, but it couldn’t escape a fundamental shortcoming:
Restriction enzymes did not evolve to make precise cuts — only to
shred foreign DNA.

As a result, scientists who used restriction enzymes for
biotechnology had little control over where their enzymes cut
open DNA.

The CRISPR-Cas system, Doudna and her colleagues realized, had
already evolved to exert just that sort of control.

To create a DNA-cutting tool, Doudna and her colleagues picked
out the CRISPR-Cas system from Streptococcus pyogenes, the
bacteria that cause strep throat. It was a system they already
understood fairly well, having worked out the function of its
main enzyme, called Cas9.

Doudna and her colleagues figured out how to supply Cas9 with an
RNA molecule that matched a sequence of DNA they wanted to cut.
The RNA molecule then guided Cas9 along the DNA to the target
site, and then the enzyme made its incision.

Using two Cas9 enzymes, the scientists could make a pair of
snips, chopping out any segment of DNA they wanted. They could
then coax a cell to stitch a new gene into the open space.

Doudna and her colleagues thus invented a biological version of
find-and-replace — one that could work in virtually any species
they chose to work on.

As important as these results were, microbiologists were also
grappling with even more profound implications of CRISPR. It
showed them that microbes had capabilities no one had imagined
before.

Before the discovery of CRISPR, all the defenses that microbes
were known to use against viruses were simple, one-size-fits-all
strategies. Restriction enzymes, for example, will destroy any
piece of unprotected DNA. Scientists refer to this style of
defense as innate immunity.

We have innate immunity, too, but on top of that, we also use an
entirely different immune system to fight pathogens: one that
learns about our enemies.

This so-called adaptive immune system is organized around a
special set of immune cells that swallow up pathogens and then
present fragments of them, called antigens, to other immune
cells. If an immune cell binds tightly to an antigen, the cell
multiplies.

The process of division adds some random changes to the cell’s
antigen receptor genes. In a few cases, the changes alter the
receptor in a way that lets it grab the antigen even more
tightly. Immune cells with the improved receptor then multiply
even more.

This cycle results in an army of immune cells with receptors that
can bind quickly and tightly to a particular type of pathogen,
making them into precise assassins. Other immune cells produce
antibodies that can also grab onto the antigens and help kill the
pathogen.

It takes a few days for the adaptive immune system to learn to
recognize the measles virus, for instance, and wipe it out. But
once the infection is over, we can hold onto these immunological
memories. A few immune cells tailored to measles stay with us for
our lifetime, ready to attack again.

CRISPR, microbiologists realized, is also an adaptive immune
system. It lets microbes learn the signatures of new viruses and
remember them.

And while we need a complex network of different cell types and
signals to learn to recognize pathogens, a single-celled microbe
has all the equipment necessary to learn the same lesson on its
own.

But how did microbes develop these abilities? Ever since
microbiologists began discovering CRISPR-Cas systems in different
species, Koonin and his colleagues have been reconstructing the
systems’ evolution.

CRISPR-Cas systems use a huge number of different enzymes, but
all of them have one enzyme in common, called Cas1. The job of
this universal enzyme is to grab incoming virus DNA and insert it
in CRISPR spacers. Recently, Koonin and his colleagues discovered
what may be the origin of Cas1 enzymes.

Along with their own genes, microbes carry stretches of DNA
called mobile elements that act like parasites. The mobile
elements contain genes for enzymes that exist solely to make new
copies of their own DNA, cut open their host’s genome, and insert
the new copy.

YouTube/McGovern
Institute for Brain Research at MIT

Sometimes mobile elements can jump from one host to another,
either by hitching a ride with a virus or by other means, and
spread through their new host’s genome.

Koonin and his colleagues discovered that one group of mobile
elements, called casposons, makes enzymes that are pretty much
identical to Cas1.

In a new paper in Nature Reviews Genetics, Koonin and Mart Krupovic of the Pasteur Institute in
Paris argue that the CRISPR-Cas system got its start
when mutations transformed casposons from enemies into friends.

Their DNA-cutting enzymes became domesticated, taking on a new
function: to store captured virus DNA as part of an immune
defense.

While CRISPR may have had a single origin, it has blossomed into
a tremendous diversity of molecules. Koonin is convinced that
viruses are responsible for this. Once they faced CRISPR’s
powerful, precise defense, the viruses evolved evasions.

Their genes changed sequence so that CRISPR couldn’t latch onto
them easily. And the viruses also evolved molecules that could
block the Cas enzymes. The microbes responded by evolving in
their turn. They acquired new strategies for using CRISPR that
the viruses couldn’t fight.

Over many thousands of years, in other words, evolution behaved
like a natural laboratory, coming up with new recipes for
altering DNA.

The Hidden Truth

To Konstantin Severinov, who holds joint appointments
at Rutgers University and the Skolkovo Institute of Science and
Technology in Russia, these explanations for CRISPR may turn out
to be true, but they barely begin to account for its full
mystery.

In fact, Severinov questions whether fighting viruses is the
chief function of CRISPR. “The immune function may be a red
herring,” he said.

Severinov’s doubts stem from his research on the spacers of E.
coli. He and other researchers have amassed a database of tens of
thousands of E. coli spacers, but only a handful of them match
any virus known to infect E. coli.

Flickr/Eric
Erbe/Christopher Pooley/USDA

You can’t blame this dearth on our ignorance of E. coli or its
viruses, Severinov argues, because they’ve been the workhorses of
molecular biology for a century. “That’s kind of mind-boggling,”
he said.

It’s possible that the spacers came from viruses, but viruses
that disappeared thousands of years ago. The microbes kept
holding onto the spacers even when they no longer had to face
these enemies. Instead, they used CRISPR for other tasks.

Severinov speculates that a CRISPR sequence might act as a kind
of genetic bar code. Bacteria that shared the same bar code could
recognize each other as relatives and cooperate, while fighting
off unrelated populations of bacteria.

But Severinov wouldn’t be surprised if CRISPR also carries out
other jobs. Recent experiments have shown that some bacteria use
CRISPR to silence their own genes, instead of seeking out the
genes of enemies.

By silencing their genes, the bacteria stop making molecules on
their surface that are easily detected by our immune system.
Without this CRISPR cloaking system, the bacteria would blow
their cover and get killed.

“This is a fairly versatile system that can be used for different
things,” Severinov said, and the balance of all those things may
differ from system to system and from species to species.

If scientists can get a better understanding of how CRISPR works
in nature, they may gather more of the raw ingredients for
technological innovations.

To create a new way to edit DNA, Doudna and her colleagues
exploited the CRISPR-Cas system from a single species of
bacteria, Streptococcus pyogenes.

There’s no reason to assume that it’s the best system for that
application. At Editas, a company based in Cambridge,
Massachusetts, scientists have been investigating the Cas9 enzyme
made by another species of bacteria, Staphylococcus aureus.

In January, Editas scientists reported that it’s about as
efficient at cutting DNA as Cas9 from Streptococcus pyogenes. But
it also has some potential advantages, including its small size,
which may make it easier to deliver into cells.

To Koonin, these discoveries are just baby steps into the ocean
of CRISPR diversity. Scientists are now working out the structure
of distantly related versions of Cas9 that seem to behave very
differently from the ones we’re now familiar with. “Who knows
whether this thing could become even a better tool?” Koonin said.

And as scientists discover more tasks that CRISPR accomplishes in
nature, they may be able to mimic those functions, too. Doudna is
curious about using CRISPR as a diagnostic tool, searching cells
for cancerous mutations, for example. “It’s seek and detect, not
seek and destroy,” she said.

But having been surprised by CRISPR before, Doudna expects the
biggest benefits from these molecules to surprise us yet again.
“It makes you wonder what else is out there,” she said.