A ribosome (gray) creates a protein by translating the genetic code within an mRNA molecule (blue). Once it reaches the stop signal, it releases the protein (orange) and is “recycled” by Rli1 by being split into two pieces. [Nicholas Guydosh, Johns Hopkins Medicine]
A ribosome (gray) creates a protein by translating the genetic code within an mRNA molecule (blue). Once it reaches the stop signal, it releases the protein (orange) and is “recycled” by Rli1 by being split into two pieces. [Nicholas Guydosh, Johns Hopkins Medicine]

Ribosomes, normally obedient to stop and start signals on messenger RNA, occasionally “go rogue.” They take it upon themselves to build proteins beyond the usual coding sequence, overrunning a portion of the 3′-untranslated region (3′-UTR).

A rogue ribosome lightens its load first, however. It releases the protein that it strung together while passing over the coding sequence. Only then does it resume its translational ways, creating a short, detached protein, not a short appendage to the “proper” protein.

Rogue ribosomes have made themselves known to researchers at the Johns Hopkins School of Medicine. These researchers, led by Rachel Green, Ph.D., suggest that rogue ribosomes become impatient. When they finish translating messenger RNA’s coding sequence, they wait to be recycled—but only for so long.

Previous studies had shown that Rli1 can split ribosomes into their two component parts once they encounter a stop code and are no longer needed. This “recycling” process, they say, disengages a ribosome from its current mRNA molecule so that it's available to translate another one. But it was unclear whether Rli1 behaved the same way in live cells.

To find out, the researchers deprived living yeast cells of Rli1, predicting that translation would slow down as ribosomes piled up at stop codes. To “see” where the ribosomes were, the team added an enzyme to the cells that would chew up any exposed RNA. The RNA bound by ribosomes would be protected and could then be isolated and identified. As predicted, the depletion of Rli1 increased the number of ribosomes sitting on stop codes. But they also saw evidence of ribosomes sitting in the untranslated region, which they called a surprise.

The details of this work appeared August 13 in the journal Cell, in an article entitled, “Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo.”

“When Rli1 levels were diminished, 80S ribosomes accumulated both at stop codons and in the adjoining 3′-UTRs of most mRNAs,” wrote the authors. “Frequently, these ribosomes reinitiated translation without the need for a canonical start codon, as small peptide products predicted by 3′-UTR ribosome occupancy in all three reading frames were confirmed by western analysis and mass spectrometry.”

“Eliminating the ribosome-rescue factor Dom34 dramatically increased 3′-UTR ribosome occupancy in Rli1 depleted cells, indicating that Dom34 clears the bulk of unrecycled ribosomes,” the authors continued. “Thus, Rli1 is crucial for ribosome recycling in vivo and controls ribosome homeostasis.”

According to Nicholas Guydosh, Ph.D., a postdoctoral fellow at Johns Hopkins and one of the co-authors, ribosomes appear to get tired of waiting to be disassembled. They decide to get back to work. And they proceed with “the protein-making work that appears right in front of them,” the untranslated region.

The purpose of these many small proteins is unknown. This uncertainty, said Dr. Green, generates a whole new set of questions for researchers. Chief among them is whether the proteins made in this unusual way have useful or damaging functions and under what conditions, questions that have the potential to further our understanding of cancer cell growth and how cells respond to stress.

It may be significant, Dr. Green pointed out, that ribosomes increase in the untranslated region when yeast are stressed by a lack of food: “It's possible that these small proteins actually help the yeast respond to starvation, but that's just a guess.”

Because ribosomes are essential to create new proteins and cell growth scientists believe the rate at which cells replicate is determined, at least in part, by how many ribosomes they have. Cells lacking Rli1 can't grow because their ribosomes are all occupied at stop codes and in untranslated regions. Thus cancer cells increase their levels of Rli1 in order to grow rapidly.

“We didn't understand previously how important ribosome recycling is for the proper translation of mRNA,” emphasized Dr. Green. “Without it, ribosomes are distracted from their usual work, which is crucial for normal cell maintenance and growth. This finding opens up questions we didn't even know to ask before.”

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