Signalling functions of polyubiquitin chains
1 PhD project offered in the IPP summer call 2019
The ubiquitin system plays a key role in determining the function and fate of proteins in virtually every biological pathway, including genome maintenance and gene expression. Most often, ubiquitin signalling is mediated by polyubiquitin chains attached to selected substrate proteins. Depending on the linkage between the individual ubiquitin moieties, such chains can adopt many distinct forms and - by means of linkage-selective downstream effectors - convey distinct biological effects. For example, polyubiquitin chains linked via lysine 48 of ubiquitin are best known to induce degradation of the modified substrate by the proteasome. However, ubiquitin contains seven lysines, and even its N-terminus can engage in the formation of linear chains, thus greatly expanding the potential range of alternative signalling functions. In many cases, the relevance of ubiquitin chain linkage is unknown, despite growing evidence that non-degradative polyubiquitylation is implicated in many human diseases such as cancer, neurodegeneration and inflammation. Understanding the impact of polyubiquitin chain linkage is therefore an important goal in biomedical research.
PhD project: Development and application of molecular tools for the in vivo analysis of polyubiquitin chain linkage
Analysis of polyubiquitin chain signalling requires tools for linkage-specific in vivo and in vitro analyses. Classically, these include antibodies, ubiquitin mutants and analytical methods such as mass spectrometry. Although antibodies have proven to be highly selective, their complex structures make them impractical for in vivo use. In our lab, we are currently developing affinity probes for major types of polyubiquitin chains that can be used as reagents for the isolation of relevant ubiquitin conjugates, as sensors to locate individual chain types within cells, or as inhibitors that prevent specific branches of ubiquitin signalling in vivo. This PhD project aims at a thorough biochemical characterisation of these probes, potentially including a structural analysis, and their application to the investigation of ubiquitin signalling in the context of DNA repair and genome stability. Using a range of methods in genetics, molecular and cell biology, the student will isolate and identify DNA damage-induced polyubiquitin conjugates in yeast and mammalian cells and investigate the consequences of the modifications as well as the relevance of their specific linkage. In this manner, we expect to gain insight into the functions of ubiquitin chain linkage in genome stability and be able to assess the potential benefits of selectively interfering with such processes.
Publications relevant to the project
Zhao S and Ulrich HD (2010). Distinct consequences of posttranslational modification by linear versus K63-linked polyubiquitin chains. Proc Natl Acad Sci USA, 107: 7704-7709
Ulrich HD and Takahashi T (2013). Readers of PCNA modifications. Chromosoma, 122: 259-274
Ulrich HD (2014). Two-way communications between ubiquitin-like modifiers and DNA. Nat Struct Mol Biol, 4: 317-324.