Analysis of ubiquitin-dependent proteolysis in Caenorhabditis elegans

The maintenance of proteostasis is a fundamental process that encompasses refolding and degradation of unfolded and damaged proteins to enable organismal development (1). In eukaryotic cells, the ubiquitin/proteasome system (UPS) is a key determinant of proteostasis by regulating protein turnover. During the past decade, detailed mechanistic insight about the UPS was revealed from extensive studies in mono-cellular systems, such as yeast or tissue culture cells. However, a further challenge is to decipher how ubiquitin-dependent degradation pathways promote cellular differentiation and development of multicellular organisms. In this chapter, we describe an in vivo assay to study protein turnover during development and in differentiated tissues in response to intrinsic and environmental challenges in the multicellular organism Caenorhabditis elegans. This assay is particularly suitable to perform large-scale genetic screens for the identification of novel proteolysis factors and pathways important for developmental processes and opens new avenues for future investigation of tissue- or development-specific proteostasis networks.