The patent was converted in August 2006, meaning the results were now publicly available. Danisco’s head of innovation, Egan Beck Hansen, had a PhD in phage biology so he understood the significance of the discovery, and agreed with Horvath it was time to publish. Horvath typically favored specialized microbiology journals, but Barrangou boldly suggested they try Science. His colleagues scoffed at the idea but Barrangou persisted. Besides, if the paper was rejected, they would only lose a few weeks and they could always resubmit elsewhere.
Horvath was listed as the senior author but Barrangou drafted most of the manuscript. “He is good at painting the big picture, I am more in the details,” Horvath told me. Barrangou and Horvath submitted their manuscript to Science in October 2006, but it was rejected. CRISPR was not the hot commodity it is today. One of the three reviewers objected that the results were not observed in the classic model bacteria such as E. coli or Bacillus subtilus. However, Caroline Ash, the editor handling the paper, told Horvath he could resubmit if they added some more data. Barrangou and Horvath set about disrupting more Cas genes to show they were involved in phage resistance, and generated more BIMs and spacer sequences. Ash accepted a revised version of the paper, which was published in March 2007—the 20th anniversary of the first report of the mysterious sequences that would become a household word.23
The Danisco team had shown experimentally that the biological function of CRISPR-Cas systems is to provide adaptive immunity in bacteria against viruses. It was the first appearance of CRISPR in the famous pages of Science magazine. More importantly, the predictions of Mojica, Vernaud, and Bolotin had been proven correct. Yogurt for the win!
Looking back, Horvath said the paper marked “a small revolution in microbiology, a new immune system but not the big revolution that occurred in 2012.” The paper immediately resonated with biochemists from the Baltics to Berkeley. Horvath and Barrangou began presenting their results on the science circuit. Over the next few years, CRISPR became a bigger and bigger deal. “We knew it was cool,” says Barrangou. “You could use it for genotyping and vaccination and cutting viral DNA.” But there were complications. “In the dairy industry, as soon as you speak about DNA, they suspect GMO manipulations and genetic engineering,” says Horvath. “It’s a sensitive topic.”
In May 2011, DuPont bought Danisco for $6.3 billion. Today, 100 percent of all commercial cultures at DuPont (and other companies) are enhanced using CRISPR screening. “Whether you have yogurt, a bite of cheese, whether you put that on your nachos or pizza or cheeseburger, in Beijing or Paris or London or New York or Buenos Aires, you are consuming a fermented dairy product that was manufactured using a CRISPR-enhanced starter culture,” says Barrangou. Today, the legacy of Barrangou and Horvath’s discovery can be found in products such as CHOOZIT SWIFT 600, one of Dupont’s most successful starter cultures, especially designed for pizza cheese. DuPont sells hundreds of starter culture packs developed from studies using Horvath’s library of some 7,000 phages.
One year after his team’s landmark paper, Horvath was asked why the Science paper had become so frequently referenced. He predicted CRISPR would have a major impact on improving the quality of functional food ingredients and a detrimental impact on the population of bacterial viruses.24 Asked whether their work had any broader ramifications, Horvath replied: “Our research does not have any social nor political implication.”
The yogurt maker extraordinaire would soon eat his words.
I. The term “CRISPR” wasn’t coined until 2001. Although the true significance of Mojica’s 1993 discovery was unknown at the time, twenty-five years later, the date would be immortalized on IMAX movie screens around the world as the opening credit in Rampage.
II. The CRISPR repeats have nothing to do with adaptation to salinity. “It is still a mystery!” Mojica says. He has yet to receive funding to study the question further.
III. Ishino is now a biochemistry professor at Kyushu University. He studies DNA repair in thermophilic archaea, and is searching for new CRISPRs.
IV. In 1997, Rhone-Poulenc split its chemical and pharma businesses to form Rhodia and, two years later, Aventis. The food company remained with chemical division.
CHAPTER 4 “THELMA AND LOUISE”
Fifteen years to the day after President Clinton’s human genome celebration in the White House in June 2000, Jennifer Doudna posed in her laboratory at Berkeley for a New York Times photographer. The background is full of typical lab paraphernalia—cubicle freezers tucked under the bench, pipettes hanging on the wall, old yellow radioactive hazard tape. Doudna looks off to the side, wearing a pinstripe double-breasted jacket while holding a pristine white lab coat (creases still visible).
The photo reminded me of a classic Time cover featuring Craig Venter during the height of the genome wars, a lab coat over half of his dark business suit, creating a distinctly Jekyll-and-Hyde appearance. Like Venter, Doudna’s brand had evolved in short order from a dedicated academic researcher working in an obscure branch of biochemistry to an international scientific celebrity credited with spearheading a transformative new field of genome science. Venter was the poster boy for fueling a biotech revolution in genome sequencing. Doudna is the face of the CRISPR revolution, developing the ubiquitous utility tool of molecular biology enabling scientists around the world to edit DNA, from classroom to clinic, and farm to pharma. Doudna’s contemplative gaze might well have signified the ethical controversies hanging in the air, weighing heavily on her shoulders. The ensuing Times story was entitled “The CRISPR Quandary.”1
I first met Doudna in 1998, her star already ascending years before she or anyone else had heard of CRISPR. Just thirty-five years old at the time, she was making her first visit to the headquarters of the Howard Hughes Medical Institute (HHMI)I—twenty manicured acres nestled in Chevy Chase, Maryland, just outside Washington, DC. On the faculty at Yale University, Doudna was a newly minted investigator of the nonprofit institute, selected after a rigorous nationwide competition as one of the most talented young scientists in the country.
Doudna had a stellar scientific pedigree, having trained with not one but two Nobel laureates. With the HHMI’s hefty financial support of about $1 million a year (a blip on what was then a $10 billion endowment), Doudna could indulge her scientific curiosity. I congratulated her on her appointment over a glass of wine. She graciously told me about her research plans. I nodded along enthusiastically, hoping my lack of structural biology expertise wasn’t too obvious.
Born in Washington, DC, Doudna was seven years old when her parents moved to Hilo, on the big island of Hawaii. Her father was an English professor at the University of Hawaii (UH) Hilo, while her mother taught history at the local community college. The Hilo scenery provided abundant plants and animals for Doudna to explore and ponder their evolution. When she was about twelve, Doudna’s father left a book on her bed—a dog-eared paperback copy of The Double Helix, Jim Watson’s riveting personal tale of the discovery of the structure of DNA. She ignored it at first, assuming it was a detective novel—which, in a sense, it was.