Decode the structure of a CRISPR system based on RNA

In recent years, CRISPR-Cas9 has gone beyond the limits of the laboratory and has become a public specialist. This CRISPR-Cas9 gene editing tool is promising for correcting defects within individual cells and potentially curing or preventing many diseases in humans. But the Cas9 system alters DNA, not RNA, and some experts believe that the possibility of modifying RNA can prove equally useful.

Scientists at the Salk Institute report for the first time the detailed molecular structure of CRISPR-Cas13d, a promising enzyme for new RNA editing technologies. They were able to visualize the enzyme through cryoelectron microscopy (cryo-EM), a cutting-edge technology that allows researchers to capture the structure of complex molecules with unprecedented detail. The results were reported on September 20, 2018, in the journal Cell.

"This article provides a molecular model for genetic engineering focused on RNA," says Dmitry Lyumkis, an adjunct professor in structure and one of the study's corresponding authors. "This adds to the extent of the tools needed to conduct this kind of crucial biomedical research."

Derived from genes originally found in bacteria, CRISPR has been described as a "molecular chisel" or "live cell word processor". It exchanges one segment of genetic code with another. In the CRISPR-Cas9 system, Cas9 is the enzyme that cuts DNA. Having editing tools for RNA, however, would allow scientists to alter the activity of a gene without making a permanent – and potentially dangerous – change to the gene itself.

"The DNA is constant, but what is constantly changing are the RNA messages that are copied from DNA," says Silvana Konermann, Research Associate at the Institute. Hugh Hughes and one of the first authors of the study. "Being able to modulate these messages by directly controlling RNA has important implications for influencing the fate of a cell."

At the beginning of the year, Patrick Hsu, member of Konermann and Helmsley-Salk, published another article in Cell discover the family of enzymes called CRISPR-Cas13d and report that this alternative CRISPR system was effective in recognizing and reducing RNA. The team also showed that this tool could be used to correct a protein imbalance causing disease in the cells of a person with dementia.

The new study, a collaboration between Lyumkis and Hsu laboratories, is based on the discovery of the Cas13d family and provides the molecular details that explain its operation.

"In our previous article, we discovered a new CRISPR family that can be used to create RNA directly inside human cells," says Hsu, who is the other corresponding author of the new job. "Now that we have been able to visualize the structure of Cas13d, we can see in more detail how the enzyme is guided to RNA and how it is able to cut RNA.This information allows us to improve the system the process is more effective, paving the way for new strategies for treating RNA diseases. "

The team used cryo-EM to reveal new details in Cas13d by freezing the enzyme in different dynamic states, allowing researchers to decode a range of activities instead of seeing an activity at a time given.

"This allowed us to see how Cas13d guides, links, and targets RNA," said Cheng Zhang, an associate researcher at Lyumkis Lab and lead author of the journal. "We hope this new knowledge will help develop the power of gene editing tools."

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More information:
Cheng Zhang et al, Structural bases of CRISPR-Cas13d RNA-guided ribonuclease activity, Cell (2018). DOI: 10.1016 / j.cell.2018.09.001