Detailed "catalogue" of degradation products in cells created

A group of researchers from Switzerland have visualised and catalogued "blueprints" that lead to defective proteins.

New insights into the quality control mechanism of cells

Cells have their own quality control mechanism to prevent the production and accumulation of harmful proteins. This quality control is essential for correct embryonic development in all mammals and plays an important role in tumours and genetic diseases such as cystic fibrosis. A group of researchers from the University of Bern and the University of Basel have now, for the first time, visualised and catalogued "blueprints" that lead to defective proteins and are normally recognised and rapidly degraded in cells. This leads to a better understanding of this degradation mechanism and helps in the development of new therapeutic approaches.

When products leave a factory, they still have to go through quality controls beforehand. Similarly, when we express our genes, there are several such quality controls to ensure that the final products, the manufactured proteins, contain no errors and are functional.

In a new study, Professor Oliver Mühlemann and his team at the University of Bern, in collaboration with researchers from the Biozentrum in Basel, have gained new insights into a quality control mechanism that removes defective gene products from the cells, thus ensuring the error-free expression of our genes. The study has now been published in the scientific journal "Genome Biology".

Quality control against defective proteins

Every cell contains thousands of different proteins, each of which fulfils a specific task. To produce a specific protein, a gene must first be copied into a molecule of mRNA (messenger RNA). This is further processed and ultimately serves as the blueprint for protein production in the cellular protein factory.

"It is important that this mRNA is produced and processed correctly - because if the blueprint contains errors, a faulty protein is produced, which poses a potential risk to the cell," says Oliver Mühlemann from the Department of Chemistry, Biochemistry and Pharmacy (DCBP) and the National Centre of Competence in Research (NCCR) "RNA & Disease". Therefore, the cell has a number of quality control mechanisms to detect and remove faulty mRNAs. One of these mechanisms, known in technical jargon as nonsense-mediated mRNA decay (NMD), specifically targets mRNAs that stop producing a protein too early. These mRNAs contain a code that signals the protein factory to stop the production of a protein too early - even before the protein has been completely produced.

Such faulty mRNAs usually arise during the processing steps that an mRNA must undergo before it serves as a finished template for protein production. One such processing step is splicing, in which certain sequences (the introns) are cut out of the original mRNA and the remaining mRNA (the exons) are spliced back together. This is because in human cells a gene is not present on the DNA as a continuous section, but is interrupted by DNA sections that are not needed for the production of a protein.

The modular structure of a gene enables different mRNA variants and thus also protein variants to arise from one and the same gene. This results in a multitude of possible combinations and proteins, which is particularly important for the evolution of complex organisms. However, this process also carries the risk of producing defective proteins.

Degradation products made visible for the first time

In healthy cells in which the NMD quality control is active, faulty mRNAs can hardly be detected because they are quickly recognised and degraded after production. How then can it be determined which mRNAs fall victim to NMD quality control? By eliminating the key players in the quality control process. Thus, the incorrectly spliced mRNAs accumulate in the cells. But here lies the next challenge: These mRNAs come from the same gene as the "correct" mRNA variants and are therefore very similar to them. With previous sequencing methods, they could hardly be distinguished.

Previous methods for detecting mRNAs in cells are based on sequencing many small sections that are later reassembled into a whole using bioinformatic tricks. Evan Karousis of DCBP and NCCR RNA & Disease, first author of the study, explains that the current study used a new method that decodes mRNAs from A to Z in one piece. "In this way, each detected mRNA can be unambiguously assigned to an mRNA variant," says Karousis. With these technical tricks, the researchers succeeded for the first time in creating an almost complete catalogue of NMD degradation products in human cells.

"Catalogue" of mRNAs for further research and development of new therapeutic approaches

This classification makes it possible to study features that distinguish NMD degradation products from "conventional" mRNAs. "If certain mRNAs accumulate that are degraded in healthy cells by NMD quality control, this can contribute to the development of tumours, as is the case with gastric cancer, for example," Oliver Mühlemann explains. So, if one understands how quality control can distinguish the faulty from the correct mRNAs, this knowledge contributes significantly to the development of new therapeutic approaches for diseases in which quality control is impaired.

Original publication:
Evangelos D. Karousis, Foivos Gypas, Mihaela Zavolan and Oliver Mühlemann: Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells. Genome Biology 22, No. 223, 13 August 2021.