About 15 years ago, a couple of food microbiologists observed that following infection the bacterial genome of certain streptococcal species integrated a sequence of the viral genome, called a spacer. This sequence served as a guide for destroying any matching DNA so that subsequent viral infections were fended off. Bacteria use this system naturally, and dairy food scientists wanted to harness it to immunize bacterial starter cultures against phage infection, a huge source of product contamination, affecting 2% of cheese production worldwide.4 In 2012, the DuPont Chemical company of Wilmington, Del., the patent holder of CRISPR-enhanced starter cultures, announced its first commercial application that could make pizza cheese consistently taste the same. It dubbed the blend of S. thermophilus strains that were used, CHOOZIT SWIFT. Given DuPont’s share of the dairy culture market, estimated to be about 50%, the chances are quite good that you have already eaten CRISPR-modified food.4 Buon appetito!
CRISPR/Cas9 is considered to be among the simplest genome-editing tools to work with because it relies on RNA–DNA base pairing, rather than the engineering of proteins that bind particular DNA sequences. This has transformed the field overnight. It used to take at least three generations of progeny to create a knockout mouse carrying the altered genetic material; with CRISPR, both gene copies are edited simultaneously, so a knockout rodent can be created in a single generation. The process has become so straightforward that an edited gene can be produced in a matter of days.
“In the past, it was a student’s entire PhD thesis to change one gene,” remarks Bruce Conklin, MD, professor of medicine at the University of California in San Francisco. “CRISPR just knocked that out of the park.”5
Talk about speed: Cas9 must identify a short three-base-pair DNA sequence immediately following the primer sequence, dubbed PAM, which occurs about 300 million times within the human genome. For it to be effective though, it must work at lightning speed, because recent studies have indicated that as many as 300,000 bindings may occur before the correct sequence of DNA is cut.6
Researchers have traditionally relied heavily on model organisms, such as mice and fruit flies, partly because they were the only species that came with a good toolkit for genetic manipulation. Now CRISPR is making it possible to edit genes in many more organisms. Researchers have begun using CRISPR to develop better biofuels and to create new enzymes for industrial markets, where they are used in laundry detergents, water treatment and paper milling. In agriculture, companies are using the system to make crops more resistant to pests and drought, without using genes spliced in from other species, such as a flounder gene inside a tomato. Livestock breeders can harness it to produce animals with more muscle mass and leaner meat, faster and more predictably than with ordinary crossbreeding.5
