T. Vomastek – eukaryotic working group
The eukaryotic working group, led by Tomáš Vomastek, studies cell signaling in higher eukaryotes, focusing on the Extracellular signal-regulated kinase (ERK) signaling pathway in animal cells.
The ERK pathway
The ERK pathway is a conserved pathway that responds to external signals by controlling cell growth, differentiation, movement, and death. The pathway’s core is made up of three protein kinases: Raf, MEK, and ERK. The signal is transmitted by a series of sequential phosphorylations, where Raf activates MEK, which then activates ERK. When ERK is activated, it phosphorylates and alters the function of many proteins, leading to a specific response to a particular extracellular signal. The activity of the ERK pathway is also subject to modulation by an accessory protein that lacks enzymatic activity. This protein can either promote the pathway’s activation (scaffold proteins) or inhibit it (protein inhibitors).
The ERK pathway also plays an important role from a biomedical point of view. Somatic mutations in Ras and B-Raf proteins that constitutively activate the ERK pathway are found with high frequency in many types of cancer, where they promote pro-oncogenic changes in gene expression, and increase cell proliferation and the invasive and metastatic potential of cancer cells.
We focus on how is ERK signaling, through phosphorylation of functionally diverse substrates, translated into specific biological responses. In particular, we study how the ERK pathway regulates the actin cytoskeleton and how this affects cellular functions such as cell proliferation, polarity, and migration. Additionally, we examine the influence of the ERK pathway and non-enzymatic scaffold proteins on the alterations in the cellular proteome, which is essential for maintaining cellular proteostasis. Our findings are also contextualized within the framework of cancer initiation and progression.
Our studies, which employed epithelial and other cell lines, demonstrated that the loss of epithelial characteristics and gain of the migratory phenotype are mediated by functionally distinct ERK substrates that control remodeling of the actin cytoskeleton and gene expression. There appears to be a hierarchy among these regulatory subprograms, which enables their coordinated execution over time. The objective of our current research is to elucidate the role of ERK substrates and scaffold proteins in the regulation of cell phenotypic changes.
Stress granules (SGs)
Our studies also concern stress-induced RNA granules and elucidation of their role in adaptation to stress conditions, using yeast and mammalian cell models. We are particularly interested in the functional and structural interplay between stress granules, P-bodies, and protein aggregates.
Stress granules (SGs) are membrane-less organelles composed mainly of ribonucleoprotein complexes that form transiently upon various environmental stresses. During their formation, SGs sequester specific mRNA molecules, removing them from active translation and allowing preferential translation of mRNA transcripts involved in the stress response. This evolutionarily conserved proteostasis strategy allows for overall cellular reprogramming of the cell during environmental stress. Processing bodies (P-bodies) are similar to SGs, but unlike SGs, P-bodies are present in unstressed cells and propagate during stress. P-bodies accumulate translationally repressed mRNA molecules and mRNA decay machinery components.
Although P-bodies’ involvement in mRNA quality control, mRNA storage, and translation repression was documented, their general function in cell metabolism remains elusive. In addition to the formation of SGs and P-bodies during environmental stress, cellular proteostasis under stress conditions is also maintained by molecular chaperones that recognize misfolded proteins. The misfolded proteins can be refolded, degraded by the ubiquitin-proteasome pathway or autophagy, or sequestered into distinct subcellular compartments where they are retained during stress to relieve an overloaded protein folding system. We aim to characterize the structural properties of SG, as well as their functional interconnection with P-bodies. We also want to determine the influence of molecular chaperones on both types of RNA granules.