Substrate binding specificity of enzymatic components of the N-end rule pathway

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Proteins rather than genes are the direct executers of manifold functions within a cell. The analysis of proteins as one of the main constituents of all living cells is therefore one of the most important tasks in biology, biotechnology and medicine. Proteins play central roles e.g. as scaffold or storage components (cytoskeleton, energy storage), as biochemical catalysts to energetically facilitate biochemical reactions and as "biosynthetic factories" for numerous additional proteins and their modifications as well as signaling molecules. It is crucial to keep the entity of all proteins within a cell (the proteome) in a physiologically functional balance. This implies that 1) the protein concentration and abundance must be regulated and 2) their degradation if necessary. In our lab, we focus on a very specific degradation pathway virtually a way to dispose of proteins. The overall process of protein recognition and degradation comprises cell biological and biochemical pathways and diverse additional enzymatically active proteins and consume a lion's share of available intracellular energy. For example, the so-called N-end rule recognizes specifically proteins that need to be degraded because their time-of-action is past or they turned to be cytotoxic. We focus on this signaling and degradation pathway which is part of the Ubiquitin proteasome system and thus of the protein quality control. For our work, we use the currently best-understood model plant, the small crucifer Arabidopsis thaliana. Currently, only very few in known about enzymatic components involved in protein degradation via the N-end rule pathway in plants and only a small number of protein targets to be degraded, the so-called substrates. Current research publications give hints that these processes regulating protein stability play central roles in developmental and cellular biology. These processes comprise both the endogenous as well as environmental molecular communication of the plant. Examples are amongst plant infection by pathogens, during flooding situations, in cell division, seed germination and breakdown of storage proteins and lipids, i.e. altogether areas with high relevance for basic and applied plant science but also for plant-based biotechnology and agriculture. The here proposed projects deal with the analysis of a so-called E3 Ubiquitin protein ligase, PROTEOLYSIS 1, which recognizes substrates and routing them for degradation. Our studies aim at characterizing the molecular recognition mechanism by enzymes of the N-end rule pathway and by this deliver for the first time a functional analysis of enzymatic components of this protein modification pathway in plants.