Anti-CRISPRs Could Fine-Tune Genome Editing

Everything needs an off switch. I would have been bankrupt a long, long time ago if I could not turn off the lights in my apartment and C-3PO would have quickly worn out his welcome if he could not shut himself down like he did in Ben Kenobi’s hut. The important thing to remember here is that these things are useful most of the time: light helps me to see but it would not do me any good in the daytime, and C-3PO is like a sassy Google Translate…sometimes too sassy though. And it turns out that even the genome editor CRISPR-Cas9 has an off switch.

Maybe this is the first biology piece you have read in the last three years. If so, you may not know about CRISPR-Cas9 and the genome editing revolution. Commonly referred to as simply “CRISPR” in the popular press, CRISPR-Cas9 is a laboratory method for editing the DNA sequence in a living organism. Throughout the last several years, CRISPR-Cas9 has shown itself time and time again to be a simple and effective way of changing the genome of many different organisms. One group even pursued a controversial study that edited non-viable human embryos, showing that the method can likely be used to edit viable human embryos–as well as setting off a firestorm in the popular press and a lot of ethical hand-wringing within the biomedical community.

The CRISPR-Cas9 system was originally discovered in bacteria, and it functions a kind of anti-viral immune system in bacteria. As I have written before, viruses do their job by injecting a genetic material–DNA in some cases–into a host cell. Some viruses specifically target bacteria. Much like our bodies have evolved defenses against pathogens, bacteria have evolved defenses against viral invaders. This is where CRISPR-Cas9 comes in. Scientists–at a yogurt company of all places–discovered pieces of viral DNA in the genome of a bacterial species that is normally used in yogurt-making. Interestingly, bacteria with these viral signatures were also immune to the corresponding virus. Later work showed that these stretches of viral DNA were actually added to the bacteria’s genome after a viral infection. After that initial infection, the new viral DNA pieces in the bacterium could be made into RNA and loaded onto the protein Cas9. The RNA-Cas9 complex is then free to go bind to DNA that is specified by the RNA, which would be viral DNA in this example. After seeking out complementary DNA from an invading virus, Cas9 performs its molecular function: cutting that DNA into pieces that cannot take over the host cell.

Research on CRISPR-Cas9 has been moving forward at a rapid pace, so I could write exclusively about it and never run out of things to talk about. But a recent published result showed that some bacterial viruses have evolved special proteins to inactivate Cas9, effectively shutting down the CRISPR-Cas9 immune system. It has been known since the middle of the 20th century that protein activity can be controlled by the binding of another molecule. The phenomenon is broadly known as protein regulation, and it is useful because a cell often needs to fine-tune the activity of certain proteins in order to survive. For example, Escherichia coli bacteria prefer to use glucose sugar for energy, but they also can also produce an enzyme to utilize another sugar, lactose, for energy. Interestingly, a lactose molecule can bind to the protein that prevents the production of the lactose-digesting enzyme and allow for the utilization of lactose. Similarly to how lactose can control the protein that shuts down lactose metabolism, scientists recently discovered that a group of viral proteins can shut down Cas9. Importantly, they showed that the “anti-CRISPRs,” as they dubbed the molecules, can bind to the RNA-Cas9 complex and strongly inhibit the DNA-cutting activity of Cas9 in a test tube.

However, the real appeal of CRISPR-Cas9 is not that we can mix it with DNA in a test tube and see DNA cleavage. Instead, we can do all of this in a living cell and cause DNA mutations that can be useful for research or maybe even therapy. If we are going to continue using CRISPR-Cas9 in living cells–perhaps someday therapeutically–we are going to want to fine-tune its activity. Luckily, these same researchers showed that anti-CRISPRs can block CRISPR-Cas9 genome editing in human cells. This result could someday help to avoid “off-target effects” that CRISPR-Cas9 sometimes causes, which are basically just unintended editing effects that could cause more harm than good.