April 7th, 2017
(written by lawrence krubner, however indented passages are often quotes). You can contact lawrence at: firstname.lastname@example.org
But every time Mojica and his colleagues repeated the experiment, the same pattern—30 or so bases that appeared over and over again, separated by lengths of seemingly unrelated DNA—reappeared. Reading journal articles in the library, Mojica learned that a Japanese group had noticed something similar in the genome of E. coli a few years before. Despite the fact that the repetitions did not seem to be connected to H. mediterranei’s predilection for salt, he put a chapter on them at the end of his Ph.D. thesis. And by the time he turned the thesis in, he couldn’t stop thinking about them.
The answer seemed to be stranger and more profound than he had ever dreamed of.
There weren’t many people who shared his interest. Unexplained oddities are common in the genomes of most organisms, from humans to archaea, the group of microorganisms to which H. mediterranei belongs. Even after moving on to other subjects, Mojica remained fascinated by the fact that E. coli and H. mediterranei, which were only distantly related, both had repeats—and that the “spacer DNA” between the repeats was always about the same length despite having a wide variety of different sequences. What were these things for?
In 1994, between a pair of short-term positions, he returned to these single-celled curiosities and inserted extra copies of the repeats and spacers into H. mediterranei to see what would happen. The cells promptly died—“It was amazing!” he recalls fondly—and he wrote a paper suggesting the extra copies interfered with the cells’ ability to reproduce correctly. (He was wrong.) After he was hired to teach at University of Alicante in 1997, he tried, fruitlessly, to see if the same thing would happen in E. coli. Perhaps the repeats formed small loops in the genome for proteins to attach to? (Wrong again.) “Nothing worked,” he says.
Still, in the years since he’d started his work, genome sequencing had gotten much easier. By the early 2000s, other people were starting to wonder about both the patterns that had intrigued Mojica and the genes around them, including Roger Garrett at the University of Copenhagen, Ruud Jansen at Utrecht University in the Netherlands, and Eugene Koonin at the Unites States’ National Center of Biotechnology Information (NCBI). When Mojica and Jansen struck up a correspondence, they began tossing around catchy names for the patterns, and on Nov. 21, 2001, they settled on CRISPR—an acronym for Clustered Regularly Interspaced Short Palindromic Repeats.
Mojica finally found the key that was to unlock the origin of the spacers, and, along with it, the meaning of the puzzle that had transfixed him for so long, in 2003. While studying E. coli, he realized that the spacers were pieces of DNA from viruses that were retained in the genome of the host species—and that some of the microbial strains that carried the spacers were either already known to be resistant to infection or had no record of ever being infected.
What if, he wondered, the repeats, spacers, and associated genes didn’t have to do with reproduction or any of the other hypotheses that had been advanced over the years? What if, instead, the repeats were a type of adaptive immune system, used by hosts to recognize attackers by their DNA? Nothing like that had ever been seen, or even looked for, in a microorganism. Mojica was overcome, and found himself with tears in his eyes. It had been 10 years since he wrote about these curious repeats in his thesis. If his theory was correct, the answer seemed to be stranger and more profound than he had ever dreamed of.
In 2005, Mojica and his group published a paper in the Journal of Molecular Evolution with this hypothesis, and the following year, Koonin and his colleagues at the NCBI laid out in more detail just how such a system would work. In 2007, researchers at the Danish-based food and enzyme company Danisco confirmed that CRISPR did indeed represent a microbial immune system. In the following years, groups of researchers around the world described how bacteria and archaea collected viral DNA and how the subsequent destruction of invading viruses worked.