Beyond autophagy: The relevance of small ubiquitin-like modifiers for fundamental cellular processes unrelated to autophagy.
Autophagy is a highly conserved process in eukaryotes of breaking down cellular components. It plays an important role in the basal turnover of intracellular proteins and organelles, as well as in the production of amino acids under starvation conditions. In this context, the contribution to protein degradation by autophagy is equivalent to that of the ubiquitin-proteasome system. Abnormalities in the regulation of autophagy can lead to various diseases, e.g. neurodegenerative diseases. Furthermore, autophagy plays an important role in antigen presentation or degradation of invasive pathogens. Autophagy requires a whole set of so-called autophagy-related (Atg) proteins, whereby in higher organisms entire protein families have evolved in some cases out of a single ancestral Atg protein.
One such example is the Atg8 protein family, an interesting family of small ubiquitin-like modifiers, which in yeast has only one member. Two subfamilies, the LC3s and the GABARAPs, with a total of seven paralogs exist in humans. Among the multiple functions already described for human ATG8 proteins, their involvement in autophagy is best characterized. Initially, however, GABARAP and its paralogs were described for their involvement in intracellular vesicular transport processes and surface expression of receptors. Due to their high structural similarity, the precise functions of the GABARAP subfamily and especially the contribution of its individual members during these processes are poorly understood to date.
Our goal is to identify unique functions of GABARAP-type proteins beyond autophagy. We are interested in intracellular transport and degradation processes of surface proteins such as receptors and transport channels, but also in processes of unconventional protein secretion, which are no less important for the maintenance of general cell viability.
(Funding: SFB 1208)
Viral non-structural and accessory proteins are masters of manipulation: How viruses use host cell processes to their benefit.
We are studying HIV, HCV and DENV encoded proteins and their interaction with host cell components. In this way, we intend to define new targets for innovative therapies, with the aim of preventing replication but also immune evasion of the viruses. For example, hepatitis C virus (HCV) causes diseases such as chronic hepatitis, liver cirrhosis and liver cancer. In HCV infected cells, the tyrosine kinase c-Src, which normally regulates basal processes such as cell growth and differentiation, is recruited to the viral replication apparatus by two HCV proteins, NS5A and NS5B. If c-Src is unavailable, viral replication is shown to be severely diminished.
We aim to reveal the molecular basis of the underlying interactions by a structural analysis of the complex of c-Src, NS5A and NS5B.
(Funding: SFB 575, SFB974, MOI IV).
To address our questions, we apply a broad spectrum of methods. We express and purify proteins, analyze protein-protein interactions and - in cooperation - are interested in structural details of protein complexes. We use cell culture systems, edit genomes using CRIPSR/CAS9 technology and isolate and characterize extracellular vesicles. We determine selected proteomes and proxitomes in cooperation and analyze them depending on the research question. We use a wide variety of microscopy systems to make statements about, for example, cell health on a single cell basis, the dynamic localization of proteins after various stimuli and the spatial proximity of two proteins to each other. This is also often done in close cooperation. We also participate in the development of our own antibodies and have a strong focus on the application-specific validation of these antibodies.