When bacteria survive a run-in with a virus or phage, they take some of the invader’s DNA and integrate it into their own genome to help combat future attacks. HHMI investigators Eva Nogales and Jennifer Doudna have deduced molecular details of how bacteria use the RNA transcripts from these bits of DNA to target their intruder’s genome without harming their own.
In Escherichia coli, the pieces of confiscated DNA, which are integrated into clustered regularly interspaced short palindromic repeats, or CRISPRs, are transcribed as RNA and displayed on a multisubunit surveillance complex called Cascade. When Cascade encounters a piece of foreign DNA that is complementary to the CRISPR sequence it’s carrying, the complex grabs hold and targets it for destruction by a nuclease.
Nogales, Doudna, and colleagues at the University of California, Berkeley, and Wageningen University in the Netherlands, used cryoelectron microscopy to look at the structure of the Cascade complex before and after it bound to bits of foreign RNA. The scientists discovered that Cascade is shaped like a seahorse and that it displays its CRISPR-derived RNA (crRNA) in a long groove that protects the crRNA from degradation while allowing it sufficient exposure to survey the environment.
|The structure of the cascade complex bound to crRNA.|
When the complex encounters invading nucleic acids, the crRNA binds to them, forming several duplex regions. These short helical segments reduce the overall length of the crRNA, causing a conformational change in the Cascade molecule that may serve as a signal for a nuclease to destroy the invading nucleic acids.
|Structural changes that occur in Cascade when it binds to RNA.|
The structure, which was reported in the September 22, 2011, issue of Nature, may provide a way for humans to combat harmful bacteria. “Anything that allows us to understand the mechanisms by which a bacterium is able to survive viral infection means that we have a potential way to control bacterial populations by reducing their defense capabilities,” says Nogales. “The enemy of our enemy is a friend.”
Next, Nogales and Doudna want to look at the interaction between Cascade and the nuclease to learn more about the events surrounding degradation of the foreign DNA.