Banfield’s expertise in cataloguing the vast diversity of microbial life—“the weight of evolutionary history” as she calls it—promises to unearth many new tools for the CRISPR toolbox. In 2013, Kim Seed and colleagues at Tufts University made a remarkable discovery: a phage that has pilfered CRISPR repeats from bacteria—like a hostage grabbing an assailant’s weapon—and turned it on the host cell.7 Banfield’s team has also discovered so-called jumbo phages—phages with giant genomes larger than some bacteria, blurring the boundary between life and death—lurking in the gut microbiome of people in Bangladesh with a non-Western diet. The CRISPR machinery not only helps the viruses evade the bacterial defense mechanisms but may also thwart competing viruses.8
It would actually be several years before the two women, both leading large groups with different research interests and areas of expertise, managed to collaborate on a research paper, but Banfield had piqued Doudna’s interest. Looking back at her pivotal role in the CRISPR drama, Banfield, one of the most accomplished microbiologists in the world, can only laugh. “One thing they’ll write on my tombstone is: ‘Told Jennifer Doudna about CRISPR-Cas.’ Like, that will be the sum of my life!”9
In the first few months of 2007, two new postdocs joined the Doudna lab. Blake Wiedenheft introduced CRISPR to the laboratory; Martin Jínek ensured the lab’s legacy.
Jínek hails from Třinec, a city on the border between the Czech Republic and Poland. One hundred miles to the west is Brno, the birthplace of genetics. Surprisingly, Jínek didn’t pay a visit to Gregor Mendel’s monastery until a few years ago, when he was invited to give a lecture. At sixteen, Jínek won a scholarship to a private boarding school in England. He then spent four years at Cambridge University studying chemistry, but always had an inclination towards biology, especially RNA, thanks in no small part of Doudna’s string of successes with Szostak and Cech. “It’s such a versatile molecule,” he told me. “It can do catalysis, fold into 3D structures, and it’s a carrier of information. It’s an all-rounder”—a term, I surmise, he picked up watching cricket at school.
After completing his PhD in Germany, Jínek wanted to study RNAi. The Doudna lab had just published the structure of an important RNA processing enzyme called dicer. Doudna likened it to a “molecular ruler” that measures RNA sequences prior to cutting them into precise lengths. RNAi was attracting huge biotech interest, underpinning new companies such as Alnylam Pharmaceuticals and Moderna. Jínek arrived in Berkeley just before publication of the Barrangou et al. Science paper, which elevated CRISPR to prime time. Doudna’s group discussed that paper in a journal club meeting. “Everybody was quite excited about it,” Jínek recalls. “We decided that this was going to be an RNA-guided mechanism, like RNA interference. There was going to be some kind of connection.”
A short time later, Wiedenheft, a swarthy scientist from Montana, visited for an interview with Doudna and talked about studying CRISPR. “We were all primed for that by the journal club—Jennifer included,” Jínek said. The man from Montana got the job and performed the first CRISPR experiments in Doudna’s lab. Wiedenheft was interested in the pathways by which phages infect bacteria and conversely, how bacteria ward off phage infection. Like Banfield, he had collected microbial samples in Yellowstone and other extreme locations. “Without Blake being in the trenches, I don’t know if the Doudna lab would’ve had a meaningful thrust in that direction,” said Ross Wilson, who joined the lab two years later.10
Jínek wasn’t working on CRISPR himself but he’d regularly talk science with Wiedenheft. The Czech’s first involvement was helping his friend learn about protein crystal structures for a first look at a DNA-cutting enzyme called Cas1, published in 2009.11 Some afternoons, the two men would take a break to go biking in the Berkeley hills. Wilson shakes his head recalling the sweaty duo returning to the lab in their spandex shorts.
Just as Doudna’s interest in CRISPR was getting off the ground, her head was turned by an irresistible offer in 2009 from one of the most famous names in biotech. She admits she was undergoing a mini midlife crisis, looking for a new scientific challenge. “Am I going to get to the end of my career and feel like I did some cool stuff, had some fun, published some papers we’re proud of, but did I really solve any problems?” she told journalist Lisa Jarvis.12
The offer came from Richard Scheller, Doudna’s former colleague at HHMI before he became head of R&D at Genentech, one of the most successful and coolest biotech companies in the world.13 Doudna would have the chance to apply her RNA expertise in the search for novel drugs and therapies. Her appointment as Genentech’s new vice president of Discovery Research was announced in a press release, and she listed her change of address in an article with Jínek in Nature.14 She hoped that most of her group would join her in South San Francisco, but industry wasn’t appealing to Jínek. Plan B was to move down the hall and finish his postdoc in the lab of Doudna’s husband.
However, Doudna soon had a change of heart. “I realized what I’m good at doing and what I really like. It all boiled down to creative, untethered science,” she said. After a somewhat painful two months, she resigned and returned to Berkeley, where she reclaimed her HHMI professorship. Having given up most of her administrative obligations, she was free to pursue “crazy, creative projects” that might not be clinically relevant but she considered cool science. And the craziest project in the lab was CRISPR. “Had I not made the foray to Genentech and then back to Berkeley, I might not have done any of the CRISPR work,” she acknowledged.15
In a 2010 lab photo, Doudna is pictured with her troop of CRISPR devotees—Wiedenheft, Jínek, graduate student Rachel Haurwitz, and longtime lab manager Kaihong Zhou. There is an air of innocence in the group, blissfully unaware of how their lives were about to change. Jínek had finally run out of independent funding after four years but Doudna was happy to keep him around. In 2011, he began searching for faculty positions back in Europe, but wanted to enjoy a last hurrah to end his Californian adventure. Jínek fancied taking a closer look at the little-known type II CRISPR system. Doudna soon offered him a gilt-edged opportunity.
It wasn’t just the Doudna lab that was struck by the Danisco CRISPR story. On May 23, 2007, just two days after the Science paper came out in print, Virginijus Šikšnys emailed Horvath to offer a collaboration. In the Lithuanian’s world, the discovery of a new antiviral defense system called CRISPR was almost as momentous as the collapse of the Soviet Union. For years, Šikšnys had been trying to understand how bacteria defend themselves against viruses. Suddenly, scientists from a yogurt company had described an entirely new bacterial immune system. It was the start of an important partnership that would have a major impact on the development of genome editing.
Vilnius, the capital of Lithuania, is not exactly the Mecca of molecular biology. When I first visited in the Spring of 2017, the main cultural attraction was the former KGB headquarters.II The city center is a curious mix of narrow medieval streets in the old town, where I washed down a pungent beaver stew with real mead, adjacent to rows of designer clothing boutiques.
The Vilnius Institute of Biotechnology is a few miles outside the city center. A chemist by training, Šikšnys built a reputation studying the 3D structure and properties of bacterial restriction enzymes (there are four thousand all told).III CRISPR offered an exciting new research opportunity. But first, he needed to transfer the CRISPR system into a bacterium other than S. thermophilus, for good reasons. “We don’t know how to make cheese and yogurt!” Šikšnys joked.