Periodic Reporting for period 2 - proteoRAGE (Unravelling the pRotein Allosterome of Gene Expression)
Berichtszeitraum: 2023-01-01 bis 2024-06-30
Proteins perform many of the chemical reactions essential to cell homeostasis, growth and proliferation. The most rapid and efficient mechanism to modulate protein activity is allosteric regulation, which depends on the direct binding between proteins and small-molecules. Since their intracellular concentration depends on environmental conditions, allosteric ligands can set responses of adaptation to the external environment independently on genetic factors. The lack of global streamlined methods to investigate allosteric mechanisms limits our current understanding of cellular physiology in health and disease. In this project we plan to elucidate how the complex network of interactions between small-molecules and proteins affects cellular responses. We will systematically measure protein structural changes produced by the binding of metabolites in the cell and which aspects of cellular activity they influence. This is important to understand the chemical reactions necessary for life and modulate them with drug molecules.
In this project we set-up the methodological framework by showing that structural proteomics can be used to identify new drug targets in human cells. We also figured that analysis of global protein structural responses are more sensitive readouts than classical protein abundance measurements for interrogating activation of biological responses in cells and tissues (Mateus, et. al. MSB 2021). This establishes the methodological background for addressing the scientific questions proposed in this project.
We carried on highlighting the importance of small molecules in modulating intermolecular and intramolecular binding interfaces between multiple proteins (Ruwolt et. al. Current Opinion in structural biology 2023). We also investigated the contribution of post-translational gene regulation in explaining transcriptional memory in Saccharomyces cerevisiae. We showed that the protein subunits of the nuclear exosome (the TRAMP and the NNS complexes) are less active in primed conditions compared to naive conditions. This decrease in protein function is consistent with a relative increase in the expression of genes sensitive to the action of the nuclear exosome. Unexpectedly, there was also a relative decrease in factors involved in cytoplasmic decay. This suggests that changes in the cytoplasmic mRNA decay may contribute to modulate transcriptional memory in yeast (Li et. al. Nature Communications, 2023).
We carried on highlighting the importance of small molecules in modulating intermolecular and intramolecular binding interfaces between multiple proteins (Ruwolt et. al. Current Opinion in structural biology 2023). We also investigated the contribution of post-translational gene regulation in explaining transcriptional memory in Saccharomyces cerevisiae. We showed that the protein subunits of the nuclear exosome (the TRAMP and the NNS complexes) are less active in primed conditions compared to naive conditions. This decrease in protein function is consistent with a relative increase in the expression of genes sensitive to the action of the nuclear exosome. Unexpectedly, there was also a relative decrease in factors involved in cytoplasmic decay. This suggests that changes in the cytoplasmic mRNA decay may contribute to modulate transcriptional memory in yeast (Li et. al. Nature Communications, 2023).
By the end of the project we will show how environmentally-driven interactions between proteins and metabolites are driving cell fate in homeostasis and during disease where protein translation and metabolic enzymes are involved.