How do cells prevent premature protein release? UIC study cracks the case

(Press-News.org) It’s known as biology’s central dogma: All living organisms’ genetic information is stored in DNA, which is transcribed into RNA, which is translated into proteins that perform nearly all essential tasks in a cell. A tiny cellular machine called the ribosome builds a protein until it’s signaled to stop, and the protein is released into the cell through a reaction with a water molecule.

But scientists have long puzzled over one detail: If all it takes is a water molecule to release the finished protein, why doesn’t it happen by accident?

Now researchers at the University of Illinois Chicago have uncovered the detailed chemical mechanism behind this process. The study, published in Science, helps answer a longstanding question in biology and clarifies how all living organisms execute protein production, one of life’s most essential processes.

From hard drive to 3D printer DNA is like a hard drive that stores an organism’s genetic information in the form of genes. Each gene contains instructions for making a specific protein, and the proteins control most of the functions in the cell, be it digestion in the gut, oxygen transfer in the blood or contraction of the muscles.

But cells can’t use those instructions directly. First, a copy is made in the form of messenger RNA (mRNA). Then the ribosome reads that mRNA and assembles the corresponding protein by linking amino acids together in a precise sequence.

“The process of making proteins is absolutely fundamental to life” said Yury Polikanov, professor of biological sciences in the UIC College of Liberal Arts and Sciences and senior author of the study.

In the cell, the ribosome and helper proteins read the “language” of nucleotides in mRNA and translate it into the “language” of amino acids in a protein.

“The ribosome is like a cellular 3D printer that actually receives the instructions from the genome and makes a protein,” Polikanov said.

The ribosome stops “printing” a new protein once it encounters a special signal in the mRNA known as a stop codon. At that point, a dedicated helper molecule called a release factor enters the ribosome and triggers the release of the finished protein from the carrier molecule holding it, called transfer RNA (tRNA).

This final step involves breaking the bond between the finished protein and the tRNA through hydrolysis, a chemical reaction with a water molecule.

Knowing when to stop “printing” a protein chain is just as important as knowing when to start, Polikanov said.

“The malfunctioning of this process can lead to pretty bad consequences,” like the production of faulty or dangerous proteins, he said. For example, mutations in stop codons can lead to fatal conditions like cystic fibrosis or Duchenne muscular dystrophy.

Getting the full picture Previously, researchers couldn’t figure out exactly what was happening during this bond-breaking release process. If hydrolysis just requires water, why doesn’t the bond break spontaneously from a random water molecule bouncing around?

Some had guessed that the release factor carried in the water molecule was what initiated the break. However, this step happened too quickly for scientists to capture and observe. Any attempt to assemble all the components in a test tube and freeze the ribosome right before “printing” stopped would result in the protein being released, Polikanov said.

Luckily, Polikanov and his lab had a trick up their sleeves. In 2022, they developed a technique to create a molecule that mimics the tRNA-protein bond but couldn’t be broken by a water molecule — it is “non-hydrolyzable.” Using the non-hydrolyzable mimic, Polikanov’s team took detailed snapshots of the protein release reaction at near-atomic resolution with a method called X-ray crystallography. What they found changed the widely accepted textbook explanation: There are no water molecules in the right place to break the bond.

Instead, the release factor causes the tRNA to change its shape just enough to unleash its hidden chemical potential. A small part of the tRNA reaches over and breaks the bond, releasing the finished protein from the ribosome.

“It’s actually kind of nudging or kicking the substrate so that it promotes hydrolysis itself,” Polikanov said.

The finding explains why the release factor is required for termination. That small nudge ensures proteins do not release prematurely and have lengths strictly defined by the corresponding genes.

The protein release mechanism uncovered by UIC researchers appears to be at work across all forms of life — from bacteria to humans, Polikanov said. It also highlights the precision and elegance of the cellular machinery.

“We uncovered how one of the most basic biological processes actually works,” said Polikanov. “It’s not just that the release factor brings the right ingredients; it repositions the existing parts so the system can finish the job by itself.”

Other UIC co-authors on the paper include Elena Aleksandrova and Egor Syroegin.

Written by Tess Joosse

END