The Microprocessor inside you

It’s a big year for microRNAs. The 2024 Nobel Prize in Physiology or Medicine went to Victor Ambros and Gary Ruvkun, who discovered the first microRNA in 1993. Today, we know that humans make more than 1,000 different microRNAS. These molecules are critical for building and maintaining healthy bodies, so it’s crucial that they’re made the right way. Errors in microRNA manufacture can put us at risk for developmental disorders, cancer, or neurodegenerative disease.

To learn how cells accurately generate a mind-boggling array of microRNAs, Cold Spring Harbor Laboratory (CSHL) Professor and HHMI Investigator Leemor Joshua-Tor focuses her attention on a molecular machine called Microprocessor (MP). MP kicks off microRNA production by trimming down longer molecules called primary microRNAs (pri-miRNAs). MP is responsible for finding and processing every pri-miRNA in the cell. That seems like a tall order, as each pri-miRNA is shaped a little differently. At the same time, MP must avoid cutting other kinds of RNA that resemble pri-miRNAs.

Joshua-Tor says pri-miRNAs all share a characteristic hairpin loop. However, that doesn’t fully explain how MP knows which molecules to cut or how it manages to cut them correctly.

For structural biologists like Joshua-Tor, seeing is understanding. So, Ankur Garg, a postdoc in Joshua-Tor’s lab, uses cryo-electron microscopy to capture extraordinarily detailed freeze frames of MP in action. “The images show MP wrapping itself around five different pri-miRNAs, each with a distinct shape,” Garg says.

See the Microprocessor (MP) intertwined with three of the five primary microRNAs (pri-miRNAs) that the Joshua-Tor lab captured. The pri-miRNAs are labeled at the top, and MP components at the bottom.

In each image, a loop of RNA nestles within the same grooves of MP. Amazingly, the shape of MP differs depending on which pri-miRNA is in its grasp. Joshua-Tor says this surprising variability prompted her team to think of MP as an octopus armed with tentacle-like proteins:

“The body of the octopus is sitting on the bottom of the hairpin, and the tentacles can go and kind of read the RNA. So, they make the same kind of interactions with the RNA. But they can move with the RNA. The RNA basically dictates to the protein where it’s going to sit.”

That flexibility explains how MP can process so many different pri-miRNAs. Still, MP is choosy, leaving many hairpin-containing RNAs untouched. By seeing exactly how it interacts with different structures, the team is able to define key features that determine which RNAs MP will cut.

Researchers can now use this knowledge to better predict which of a cell’s many strands of RNA are destined to become microRNAs. Those predictions will help paint a clearer picture of the impact these influential molecules have on health and disease.

Written by: Jennifer Michalowski, Science Writer | publicaffairs@cshl.edu | 516-367-8455

Funding

National Institutes of Health, Memorial Sloan Kettering Cancer Center, Howard Hughes Medical Institute

Citation

Garg, A., et al., “The structural landscape of Microprocessor-mediated processing of pri-let-7 miRNAs”, Molecular Cell, November 7, 2024. DOI: 10.1016/j.molcel.2024.09.008

Core Facilites

“The Electron Cryomicroscopy (Cryo-EM) Facility offers researchers access to cutting-edge technology that has made it possible to visualize complex biological systems at near atomic resolution and detail, providing novel molecular insight into human biology and disease.” — Cryo-EM Facility Manager Dennis Thomas

“The Mass Spectrometry Core Facility provides state-of-the-art quantitative analysis of proteins and peptides, protein-protein interactions, and post-translational modifications. The resource also offers the ability to detect lipids, metabolites, and other small molecules. The facility supports experimental design, sample preparation, LC-MS analyses, and data analysis and interpretation.” — Director Paolo Cifani, Ph.D.