Bacterial ribosomes: molecular collision activates protection mechanism

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Ribosomes are vitally important for all living organisms. They translate the information stored in the messenger molecule mRNA into proteins. To do this, they bind to the mRNA strand and travel along it in order to read the genetic code and link the corresponding amino acids in the correct sequence to form a protein. If a ribosome gets stuck somewhere on the mRNA, this results in defective proteins, which can be toxic for the cell. For this reason, cells possess recycling systems to detect blocked ribosomes and eliminate the defective mRNAs and proteins. In the case of bacteria, scientists did not have any clear idea before now as to how the cell detects stalled ribosomes among the large number of functioning ones. A team led by Roland Beckmann from the Gene Center Munich, in collaboration with a team of scientists led by Allen R. Buskirk and Rachel Green from Johns Hopkins University (USA), have now shown that the collision of two ribosomes plays a crucial role in the process. Furthermore, they identified the decisive enzyme for detection and rescue, as the scientists report in the prestigious journal Nature.

As several ribosomes are usually traveling along the mRNA at the same time, the unexpected stopping of a ribosome in the middle of the mRNA strand leads to a molecular crash, in which the ribosome coming behind crashes into the stopped ribosome. “For higher organisms, eukaryotes, it was already known that the collision of ribosomes activates processes that lead to the elimination of the mRNA and the potentially toxic protein,” says Hanna Kratzat, researcher in Beckmann’s team and co-author of the paper. For the factors and mechanisms involved in eukaryotes, however, there are no counterparts in bacteria. But a team led by Allen R. Buskirk and Rachel Green (Johns Hopkins University) identified, by means of genetic screening, the enzyme SmrB as the previously unknown molecular ‘rescuer’ in bacteria, which ensures that when ribosomes get stuck, they can be detected and then recycled.

Using cryogenic electron microscopy (cryo-EM) analyses, the scientists in Beckmann’s laboratory were able to uncover the mechanism by which this happens. As in eukaryotes, it is the collision of ribosomes on mRNA that triggers the rescue operation in bacteria, which can therefore be considered as a universal principle. The bacterial enzyme SmrB consists of two parts, of which one can always bind to ribosomes. As such, the scientists assume that SmrB also docks onto normally translating ribosomes and scans them, as it were, with their free part. However, the nuclease activity of the enzyme is triggered only when two ribosomes collide: “As a result of the collision, the distance between them becomes so small that the mRNA exit of the stalled ribosome docks precisely to the mRNA entrance of the ribosome crashing into it,” says Kratzat. “Then SmrB is able to interact with both ribosomes, binds precisely in this little pocket, and cuts the problematic mRNA.” After that, other mechanisms can kick in, which are responsible for the definitive degradation of the mRNA and recycling of the ribosomes. “With our results, we’ve taken an important step toward understanding how cells distinguish between functioning ribosomes and ones that need to be freed from problematic mRNA and potentially toxic protein,” says Beckmann. “The shared discovery of collision detection as a universal principle is also a wonderful outcome of the sabbatical Rachel Green spent at LMU last year.”

Kazuki Saito, Hanna Kratzat, Annabelle Campbell, Robert Buschauer, A. Maxwell Burroughs, Otto Berninghausen, L. Aravind, Rachel Green, Roland Beckmann & Allen R. Buskirk: Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Nature 2022