Project number 22

Proteome-level insight into crop responses to environmental stress through innovative biochemical and computational omics approaches

Project abstract: Plants are increasingly exposed to extreme environmental changes, with dramatic impact on crop productivity. While plant responses to abiotic stress have been explored on physiological and molecular levels, this has – especially in the context of combined stress conditions – not been extensively investigated on the proteome level. In this PhD project we aim to combine advanced mass spectrometry with novel computational approaches to map the protein response of monocot crop seedlings to a changing environment. This will yield unprecedented insight in how plants cope with stress conditions. We will use an optimized plant proteomics workflow from the De Smet lab on leaf material from seedlings grown under varying conditions (drought, heat, cold, salt and/or metal stress). We will analyse the proteome to unprecedented depth using novel algorithms from the Martens lab that allow variant and modified protein identification. We will then perform differential analyses and visualize the results to gain unprecedented insight into the variation of maize and wheat proteomes under different stress conditions. The workflow will first be optimized for maize, and then applied to the more challenging wheat (which is hexaploid and not fully sequenced). Importantly, the novel algorithms we will use do not require a fully sequenced and annotated genome. Key hubs will be functionally characterized as new leads for crop improvement.
The work will be split equally between the De Smet lab (biological part, including MS analyses) and the Martens lab (computational part). There will be constant interaction between the two labs to optimise novel tools and to interpret results in their biological context.
Collaborative research: Both labs have a collaborative track record, exemplified through joint work (Vu, Stes et al, 2016; Smith, Roberts et al, in prep, Vu et al, in prep).

Keywords
monocot crop, proteome, combined abiotic stress, comparative omics, bioinformatics

Supervisors
Ive De Smet, VIB Dept. of Pant Systems Biology, UGent, Gent
Lennart Martens, VIB Medical Biotechnology Center, UGent, Gent