Biotechnology (Commonwealth Union) – The application of mRNA vaccines on a mass scale was done during the pandemic in 2020 for Covid-19 vaccines. Human trials had been conducted on smaller scales on mRNA vaccines for certain types of cancer.
The scientists that included Marina Rodnina and Panagiotis Poulis, from the Max Planck Institute for Multidisciplinary Sciences in Göttingen, Germany, have shed light on an important aspect of how modified messenger RNA (mRNA) is translated into proteins. In a study published in Nature Communications, the team explains why ribosomes can sometimes misread modified mRNA by shifting into an incorrect reading frame. The findings also reveal how these errors can largely be prevented by carefully designing mRNA sequences.
Researchers of the study said cells make proteins by decoding messenger RNA (or mRNA) in three-letter groups called codons. Each codon specifies a particular amino acid which contributes to the formation of a protein. mRNA vaccines utilise the same process within the cell. They deliver synthetic mRNA that tells cells to make a viral protein so the immune system can recognise it and mount a protective response.
One of the hallmarks of today’s mRNA vaccines is that they replace the natural RNA building block uridine (U) with a modified version, N1-methylpseudouridine. This change helps to prevent unwanted immune activation and promote efficient protein production.
But the modification can also change the movement of ribosomes along the mRNA strand. At certain sequences, a ribosome may occasionally slip forward one nucleotide, changing the reading frame. This leads to the following codons being read incorrectly, and may lead to an incorrect protein being produced.
Now the Max Planck researchers have been able to explain the mechanisms of this reading frame shift and to identify approaches to prevent these translation errors.
To observe this process, researchers combined studies of human cells with a fully reconstructed in-vitro translation system, allowing them to pin down exactly where and when ribosomes shift into the wrong reading frame. They also employed single-molecule fluorescence microscopy to follow individual ribosomes in real time and observe the movement of transfer RNAs (tRNAs), which identify codons and deliver the corresponding amino acids during these errors.
The results unveiled its mechanism: N1-methylpseudouridine breaks the interaction between tRNA and mRNA within the ribosome, increasing the likelihood that the tRNA will slip by one nucleotide and cause a frame shift.
Poulis indicated that a significant factor was that, frameshifting occurs only at particular mRNA sequences – and these can be avoided. The team identified UUU C as a sequence prone to frameshifting when uridine (U) is replaced with N1-methylpseudouridine. By modifying the sequence from UUU C to UUC C, for instance, without altering the protein it encodes, the researchers were able to almost entirely eliminate frameshifting.
Poulis pointed out that their study provides a rule set for designing mRNA vaccines and therapeutics. Avoiding sequences that increase the risk of frameshifting could help developers minimise unintended protein products while preserving the advantages of modified mRNA technology. This approach could be applied not only to COVID-19 vaccines but also to other mRNA-based treatments, including vaccines targeting other infectious diseases and personalised cancer vaccines.
“When selecting modifications for therapeutic mRNAs, we need to consider two things: how effectively they reduce unwanted immune activation and how faithfully the mRNA is translated,” said Rodnina. They pointed out that finding out the way modified mRNAs impact the ribosome thus gives a molecular basis for the formation of the next generation of mRNA vaccines and therapeutics.
