Molecule Does More Than Slice and Dice RNA

A team of Howard Hughes Medical Institute (HHMI) scientists has solved the mystery of how cells are able to control genes selectively to regulate critical events of development. The insights are based on research, just published in the journal Science, that visualized the molecule of Dicer, an enzyme that allows cells to dissect genetic material.

With the structure of Dicer solved, Doudna’s group [Jennifer A. Doudna, a Howard Hughes Medical Institute investigator at the University of California, Berkeley -ed.] showed that the enzyme is more than a molecular cleaver — it also carefully measures and snips strands of RNA into precise increments. When Dicer cleaves large strands of RNA into smaller fragments, it initiates the process of RNA interference, which can turn genes off and thereby dictate key developmental events.
“The bottom line we’ve learned from the structure is that Dicer is a molecular ruler,” Doudna explained. “It gives us a lot of insight into how the mechanism works.”
“We knew what the protein did,” said Hannon. “We knew it was an enzyme and that it recognized double-stranded RNA and cut it into pieces. But we didn’t have any clue how Dicer made the measurement and figured out where to make the cut.”
Doudna and her colleagues solved the structure of a Dicer enzyme obtained from the parasite Giardia intestinalis using x-ray crystallography, a technique that enables scientists to construct pictures of biological molecules in superb three-dimensional detail. When crystal samples of molecules like Dicer are exposed to x-rays, the x-ray beams are scattered in a way that helps researchers define the overall structure of the crystallized protein, as was the case with Dicer. Knowing how the atoms of specific molecules are arranged permits researchers to tease out their functional features and show how they go about their business inside a cell. In the case of Dicer, it shows how the enzyme recognizes RNA and snips it into precise increments.
“The fact that it makes these specific sized RNAs is important to the process,” Doudna said. The small RNA fragments created by Dicer are then assimilated into large multiprotein complexes and guide those molecules to destinations in the cell where they turn off genes.
“The size of these small RNAs is a determinant of their function,” Hannon explained. “If the RNAs are too big or too small, they don’t make it into the effector complexes.”
Through its role in helping cells to turn off gene expression, Dicer is believed to be instrumental in initiating some of the critical processes of development. For example, scientists speculate that the RNA interference pathway plays a role in prodding blank-slate stem cells down developmental pathways to become specific kinds of cells or tissues. It may also play roles in maintaining cells, rearranging genomes and laying down the architecture of the brain, for example…
Resolving the structure of Dicer, Doudna noted, was a technical challenge as the crystals are small. But she said that the work was facilitated by access to the HHMI-supported crystallography beam lines at the Lawrence Berkeley National Laboratory’s Advanced Light Source. The synchrotron at the Advanced Light Source is capable of generating beams of x-rays to very specific wavelengths, which was critical in determining the structure of Dicer.

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