# Breakthrough DNA Editor Born of Bacteria

Interest in a powerful DNA editing tool called CRISPR has revealed that bacteria are far more sophisticated than anyone imagined.

Photo by Eric Erbe, Colorization by Christopher Pooley. USDA.

Microbes such as E. coli may use CRISPR as a weapon in their millions-year-old struggle against viruses.

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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.” Cailey Cotner Jennifer Doudna received the$3 million Breakthrough Prize for her work using CRISPR to edit DNA.

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. 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. 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.

This video illustrates how CRISPR and Cas9 can help microbes fight viruses and how researchers might use that system to edit human genes.

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.

A New Kind of Evolution

CRISPR is an impressive adaptive immune system for another reason: Its lessons can be inherited. People can’t pass down genes for antibodies to their children because only immune cells develop them. There’s no way for that information to get into eggs or sperm. As a result, children have to start learning about their invisible enemies pretty much from scratch.

CRISPR is different. Since microbes are single-celled organisms, the DNA they alter to fight viruses is the same DNA they pass down to their descendants. In other words, the experiences that these organisms have alter their genes, and that change is inherited by future generations.

For students of the history of biology, this kind of heredity echoes a largely discredited theory promoted by the naturalist Jean-Baptiste Lamarck in the early 19th century. Lamarck argued for the inheritance of acquired traits. To illustrate his theory, he had readers imagine a giraffe gaining a long neck by striving to reach high branches to feed on. A nervous fluid, he believed, stretched out its neck, making it easier for the giraffe to reach the branches. It then passed down its lengthened neck to its descendants.

The advent of genetics seemed to crush this idea. There didn’t appear to be any way for experiences to alter the genes that organisms passed down to their offspring. But CRISPR revealed that microbes rewrite their DNA with information about their enemies — information that Barrangou showed could make the difference between life and death for their descendants.

Did this mean that CRISPR meets the requirements for Lamarckian inheritance? “In my humble opinion, it does,” said Koonin.

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. 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. 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.

• David Konerding says:

I don’t think it’s true, as your title states, that nobody believed bacteria are sophisticated.

In fact, one of the primary motivations for recent work in developing minimal organisms is the recognition that E. Coli isn’t really well understood- even though it’s subject to an immense amount of experimentation, many of its most basic behaviors are just known via lab lore, and haven’t been probed at all.

People keep reporting (with surprise) that bacteria are found in ancient, inhospitable places. That’s because the entire world was transformed by, and is enervated with, bacteria, which have basically shaped the landscape, the sky, and everything underground too. They are far more complex, capable of rapid adaption as well as slow or no evolution, and moving into nearly any (even absurdly toxic) location.

• Anonymous says:

Carl, it’s great that you’re addressing the positive implications of this discovery, but what are the negative ones? Or are they too awful to name? Or do we already have enough biological tools for quietly doing damage to an individual or population, that this new-to-us one won’t really make a difference?

Who is looking at the downside of making the genome as easy to edit as it is to read? Would it be an ethics committee, or something stronger? Or is the academic genie out of the bottle, as it’s free to cavort with corporations right & left?

Do those who understand this new technology think that we are in over our species-maturity heads?
Or does it herald a utopia where everyone, no matter how genetically shortchanged, can get delivered the “smart, and kind too” genes?
Paging Ted Chiang…CRISPR’s implications are calling.

• Dr. Mito says:

Great article. The history of CRISPR-Cas is simply amazing. I am positive that a lot of research went into writing this article with such a comprehensive background. I agree that limitations could have been discussed to give a more balanced perspective. However, for a researcher starting to work with CRiSPR tech, this is a great resource. Will definitely recommend this article to my colleagues and use it as a primer to my research.

Please keep writing more articles like these.

Excellent article on complex science. Encouraging to see young scientists making exciting discoveries and being recognized for their work. I have patents and this is interesting, it is not an invention but research discovery that will change the world.

• Andy Briggs says:

What a great article about a subject I knew so little about. Congratulations on such a well-written, well-researched piece. Please keep us informed about new CRISPR developments because CRISPR is obvi0usly a huge mystery waiting to be unravelled……which of course makes for great science reading!

• Rose Campion says:

I was thinking, “damn, this is a well-written article”. Then I looked at the byline – well, of course. Congrats, CZ – job well done. You walk that line: being accessible without pandering, being technically accurate without devolving into mind-numbing detail, and strewn with clever asides (“when dirigibles ruled the skies”) that add color without being flip. Thank you.

PS: Have to note, it also presents Doudner and Charpentier in a non-sexist way – focusing completely on their accomplishment, without delving into their physical appearances, couture choices, ages, or familial statuses – pretty much what would be expected if they were XY scientists instead of XX ones. Kudos there as well.

• Joachim says:

Really great article! We also wrote a short review about CRISPR on our website (http://labiotech.eu/review-crispr-therapeutical-revolution/) but your writing style is really better, I love this article and I’ll recommend it to my team!

• eddy says:

Hmm, didn’t Carl Zimmer already write this same article for the NY Times almost a year ago?
http://www.nytimes.com/2014/07/17/science/a-call-to-fight-malaria-one-mosquito-at-a-time-by-altering-dna.html
“Although research on this procedure, known as Crispr, is in its infancy, the authors of the new papers say it warrants a public discussion right now. Using the approach to genetically engineer wild species could be a boon to humanity on some fronts, but it could also lead to a broad spectrum of unplanned ecological harm”, lather rinse repeat.

• Светлана says:

I think it is worth more global view of the issue. What will happen to mankind if we begin to change the DNA?

• Tina says:

There are definitely major implications for humanity as a whole when we learn how to harness the power of CRISPR for ourselves. Someone will definitely need to look at those, and with great power absolutely comes great responsibility. Something like this will likely need to be heavily regulated and protected.

As a person with chronic disease, however, I can’t help but immediately consider the benefits of having such mastery over our own DNA. Medicine has yet to sufficiently address the complexity of chronic disease. It’s bad enough that it is complex in one person, but for every person to have slightly different mechanisms and environment driving the same diseases is why medicine is pursuing the “personalized medicine” angle so fiercely. I’d like to think that if we can simply edit out the gene mutations we know are causing problems, we could…dare I say it…actually cure diseases that aren’t infectious for once.

I hope we make such progress within my lifetime. The effects of CRISPR would be vast and wide, and I hope while we are discussing the ethics of this, we will still use it to try and help those facing chronic illness right now…and argue about the details after the fact.

• Mott Greene says:

In re title

One may say “borne by” and one may say “born of” but not, I believe, “borne of.” Borne is the past tense of bear, ” to carry”, and “born” means something rather different, i.e. “brought into existence.” Probably both are true here- the bacteria carry them, and create them, but these are two different processes ( which is the point of the article in re bacterial vs out immune systems).

• Michael Moyer says:

@Mott Greene
Thanks for your comment re: “borne.” Both “borne” and “born” are past participles of the verb “bear.” Current American usage dictates that “born” be restricted to the single use of describing a birth in the passive voice (“she was born in 1999”). “Borne” is used in all other cases, including that of the past tense of bringing about, which is what our headline describes—how CRISPR was long ago “borne” of bacteria.

• ron fucci says:

Doesn’t this kind of discovery also lead to the question of what is a genome and what are the boundaries for a genome for an organism? Also when we say immunity and infection aren’t the same questions raised – that is – what we say is an ‘infection’ may be part of a generalized process of information sharing (horizontal gene transfer) between what we now call ‘organisms’? Can an ‘infection’ be ‘good’ or ‘normal’? Perhaps the knowledge of HGT may lead us to think that life is much bigger than any one organism – information encoded in genes is transferring across what appear to be organism boundaries – perhaps how it all works, including evolution, is not quite what it seems. And what we have now is an imperfect understanding of life and information transfer between the manifestations of life

• Aleck Alexopoulos says:

Another excellent and very informative article by CZ.
AA

• César Díez says:

"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."

In some of those previous papers, the hypotesis of CRISPR as a immune system was clearly stated. It was not an idea of Kooning. For example you can read this abstract: http://www.ncbi.nlm.nih.gov/pubmed/15791728
In this paper we even stated that CRISPR mechanism could be similar to the functioning of iRNA. Kooning took that hypotesis to propose a role for Cas proteins according to iRNA mechanism, that turned out to be wrong.

I already had helped stablishing CRISPR as a family of repeats across Bacteria and Archaea, and had the idea of them functioning as an immune system. And I don't agree with others stealing the credit for that.

• Fantastic post but I was wondering if you could write a litte more on this topic?
I'd be very grateful if you could elaborate a little bit more.
Thanks!

• Denis DuBay says:

Would appreciate feedback if CZ or others could explain the specific role of the CRISPR sequence in this business? This article does an outstanding job of describing how the spacers and Cas genes work, but very little is said about the role of the CRISPR sequence itself.

Also, is anyone looking into whether remnant CRISPR-Cas-like assemblages exist (and function?!) in the human genome? If something this powerful is so ubiquitous in the bacterial genome, might it also exist in multicellular species, or do we have evidence it evolved in bacteria after the split that led to multicellularity?

Is CRISPR-Cas at all involved in enabling bacteria to swap genes with one another?

Finally, this seems to be such an effective and rapid evolutionary mechanism, do we have any evidence that it swamps traditionally-understood Darwinian selection that depends on random mutations and must work with entire populations over many generations) as an evolutionary force in the bacteria?

• Elena Sancho says:

Nice article. Have you seen recent review in Cell by Eric Lander

Eric Lander on the scientists that discovered CRISPR:
http://www.cell.com/cell/fulltext/S0092-8674(15)01705-5

Just like César Diez comments a lot of credit should be given to Mojica
http://www.ncbi.nlm.nih.gov/pubmed/15791728

• Callum says:

To state that no one actually invented Crsipr as a genome-editing tool is not true. While Crispr is a natural occurring system in prokaryotic cells it took some specific engineering to get it to work in eurokaryotic cells. The crispr scientists are using for genome editing is not the natural occurring. That would be like saying the aeroplane was not invented because birds can fly.

I think the bigger issue is why Crispr has received so much limelight compared to TALEN, and previously before that the engineered Zinc fingers. Sure it is easier but there are entire industries surrounding TALEN which does all the hard work for you. So then it is cheaper, meaning more labs have access to the technology. From the science communication it does seem that the message being put forward is that this is the first time humans can make site-specific genetic modifications rather than saying actually, this technology has been around for decades just it has got easier.

It terms of financial reward I can see why Berkeley and Broad are fighting it out in the courts but in terms of the scientific kudos, I don't get what the hype is all about. Especially since most of the hard work was done previously to the Berkeley and Broad groups.

For me the biggest conceptual jump and intellectual breakthrough was looking at these seemingly uninteresting interspersed repeated pieces of DNA and thinking it was a defence mechanism. One the biochemistry was elucidated was it really a massive conceptual leap or breakthrough for Doudna/Charpentier and Zhang to co-opt it into eukaryotic cells as genome-editing tool??

• Paul Cotter says:

A magnificent article – it makes a complex/complicated subject easy to understand.
It somewhat reaffirms what I am thinking: we are a minor subset in a sea of biological diversity.
We are a recent species to the Universe and our DNA & immune system hasn't had suffiencent time to mature (yet we are host to thousands of bacteria which are billions of years old).

You scientists need all the encouragement we can give you. Don't stop now – keep going.

• Angela Simms says:

I love this New Research, Between Bacteria & cells. all of your people done excellent work and would love to learn this. I know very complex but not hard to understand.I'll
back you people up at CRISPR Natural History.

• Anthony Cusano says:

This is a great discovery, but given the highly evolved and balanced complexity of the human, not to mention bacterial organism, the risks of CRISPR technology in suddenly altering that evolved balance are huge. I would say it is scientistic and promethean to believe that the use of CRISPR will progress risk free.

This could easily explain the Fermi paradox. Highly sophisticated civilizations never make it far enough to communicate with the rest of life in the universe because they discover technology that rapidly unravels the balance that evolution slowly brought to them.