TERMINATOR · Ribosomal frameshifts as a novel mechanism to control RNA turnover in stress

Ribosomal frameshifts as a novel mechanism to control RNA turnover in stress

We were interested to investigate cellular response to changes in the environment, by watching how the cell degrades its mRNAs. mRNAs are used to make proteins, and the type of mRNA produced will affect the types of proteins synthesized. The cell continuously synthesizes and degrades these molecules. When a cell is exposed to stress, it will need to synthesize other types of proteins, and, hence, it should get rid of the old mRNAs very fast. We suggested a possible mechanism that could lead to such a clean-up, associated with the movement of ribosomes - the machinery that synthesizes proteins. The ribosomes move along the mRNA molecule one codon at a time, and in each movement incorporate a new amino acid to the growing protein chain. However, if the ribosome “slips” one nucleotide, i.e. when its frame is shifted, it will start producing a wrong protein and will terminate at a premature termination codon (PTC). The latter is usually noticed by the nonsense-mediated decay (NMD) machinery. NMD normally degrades erroneous transcripts. However, we hypothesized that the cell uses NMD to also degrade normal mRNAs as a response to stress, via genome-wide ribosomal frameshifts. Previous work had shown mRNA degradation and ribosome movement are coupled, and that degradation intermediates are a “living trace” of how the ribosome moves in the cell. Therefore, we used a novel technology - 5PSeq - to look into these degradation intermediates and make inferences regarding movement of the ribosomes on those mRNAs that are getting degraded. Understanding how the cell responds to stress and treatment is an important milestone in science to investigate mechanisms of disease development and efficacy of drug treatments. mRNA degradation is only one of the processes that can provide better assessment of response mechanisms. It has, however, the advantage of showing fast cellular responses, as responses that occur at transcriptional, epigenetic or genetic levels occur at longer timescales. The overall objective of this work was to look at the mRNA degradation intermediates with a new technology called 5PSeq, and develop novel data analysis methods to investigate cellular response to stress. In the course of this project, we also expanded this work by investigating that same process in bacteria. By doing so, we discovered that mRNA degradation is coupled with the process of translation not only in eukaryotes, but also in prokaryotes. This enabled us to develop a technology that opens novel avenues for understanding bacterial response to antibiotic treatment, enabling more efficient diagnostics and drug discovery workflows.

Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз