Project number 6

Advanced proteomics to combat parasitic plant infestations

Ubiquitination, being the covalent attachment of a small protein, ubiquitin, to target proteins, plays an essential role in plant hormone signalling. The classical view on ubiquitination – which was the subject of the 2004 Nobel Prize in Chemistry – is that this modification leads to protein degradation, nonetheless numerous studies showcased non-degradative roles for ubiquitination. Lysines are considered to be the prime targets of the ubiquitination machinery however, some studies also suggest non-canonical ubiquitination sites including cysteines and protein amino termini, though tools are lacking to analyse these particular events on a large enough scale.
Both labs have introduced a novel proteomic technology for studying protein ubiquitination based on peptide chromatography (Walton et al., Plant Cell 2016). Here, we intend to supplement this technology with new tools for quantifying differences in the overall level of ubiquitination on a proteome-wide scale and we will develop new tools for the specific analysis of non-lysine ubiquitination events. All of these proteomic technologies will be applied for unravelling strigolactone signalling. Besides plant hormones, strigolactones act as rhizosphere molecules to serve as germination stimulants for parasitic plants. As a result, they form the molecular basis for huge crop losses. Understanding how strigolactone signalling happens at the protein level will provide the foundation to develop new molecular tools to stop parasitic plant infestations.
This project is a 50/50 distribution between the Gevaert Lab (proteomics) and the Goormachtig lab (plant genetics and molecular biology). Both labs have experience in guiding PhD students together.

Keywords
proteomics, ubiquitination, strigolactones, Arabidopsis, parasitic plant infestation

Supervisors
Kris Gevaert, VIB Medical Biotechnology Center, UGent, Gent
Sofie Goormachtig, VIB Dept. of Plant Systems Biology, UGent, Gent