Our group focusses on the effect of sodium in plants. Soil salinization leads to massive decreases in crop yield and threatens 7% of arable land and even 30% of irrigated soil. This decrease in yield is caused by (1) a reduced uptake of water due to osmotic effects and (2) inhibition of certain cellular processes, like photosynthesis, by the replacement of potassium by sodium ions.
Plants developed specific mechanisms to deal with sodium stress, meaning that sodium ions must be perceived. Although scientists have been searching for this sensor since the early days of molecular biology, this sensing mechanism remains undiscovered to date. Sensing mechanisms have been discovered in cyanobacteria, Caenorhabditis elegans and mammals (like our taste receptors on our tongue), but no homologous genes are found in plants.
However, genetic evidence and in silico studies of our collaborators at UvA hint at a specific protein domain that could be a sodium sensor. Hence, I propose to study the sodium binding properties of this domain in vitro using ITC. Initially, we will study the domain from Arabidopsis thaliana proteins, but if our hypothesis is correct and time allows, crop species will be used to test whether this is a conserved function. Modified proteins will also be tested to verify which amino acids are required for the binding of sodium. The thesis will include: the creation and validation of the pipeline, cloning the constructs and mutations and tertiary structure analysis. Also helping our collaborators with the analysis of in silico studies is discussable, as are your own ideas or skills. Depending on the outcome of this study, we can also perform (1) Y2H assays to study the interactions of known downstream targets, (2) study sodium binding properties using fluorescent dyes, (3) start in planta work.
Techniques will include: Cloning, Isothermal titration calorimetry, in silico studies, confocal imaging and Y2H