Under supervision of: Kilian Duijts (email@example.com) and Aalt-Jan van Dijk (Bioinformatics)
Aim: In silico prediction of protein dimerization using structural modeling approaches and in vitro/in planta prediction validation.
Soil salinity is an increasing problem for agriculture worldwide. To understand how plants deal with this stress we study the development of their root systems under salinity stress. Salinity stress alters the expression and potentially the activity of numerous (root) developmental transcription factors. In this thesis/internship you will be studying the dimerization affinity of two potential regulators of root development under salt stress.
In previous experiments we have identified a salt induced transcription factor (SIT1) that is involved in lateral root development during salt stress, and in consequent Y2H and BIFC experiments SIT1 has been shown to interact with other transcription factors in this family, some of which are also involved in stress responses. In this thesis you will use bioinformatic structural protein modelling tools to predict what residues facilitate this interaction. Next you will use molecular cloning techniques to do site directed mutagenesis on these residues and transient gene expression to test their interaction in vivo.
Are you interested in doing a thesis or internship on the intersection of bioinformatics and molecular biology? Don’t hesitate to get in touch!
- Structural protein modeling
- BIFC/split luciferase assays
- (confocal) microscopy
- N. benthamiana agrobacterium infiltration and/or
- protoplast isolation and transfection
- Lavenus, Julien, et al. “Lateral root development in Arabidopsis: fifty shades of auxin.” Trends in plant science 18.8 (2013): 450-458 https://dx.doi.org/10.1016/j.tplants.2013.04.006
- Banda, Jason, et al. “Lateral root formation in Arabidopsis: a well-ordered LRexit.” Trends in plant science 24.9 (2019): 826-839, doi:10.1016/j.tplants.2019.06.015.
- Evans, Richard, et al. Protein Complex Prediction with AlphaFold-Multimer. 2021, doi:10.1101/2021.10.04.463034
- Grefen, Christopher, and Michael R. Blatt. “A 2in1 Cloning System Enables Ratiometric Bimolecular Fluorescence Complementation (RBiFC).” BioTechniques, vol. 53, no. 5, 2012, doi:10.2144/000113941
- Pandey, Shashank K., and Jungmook Kim. “Coiled-Coil Motif in LBD16 and LBD18 Transcription Factors Are Critical for Dimerization and Biological Function in Arabidopsis.” Plant Signaling & Behavior, vol. 13, no. 1, NLM (Medline), Jan. 2018, p. e1411450, doi:10.1080/15592324.2017.1411450.
- Karlova, Rumyana, et al. “Root plasticity under abiotic stress.” Plant Physiology 187.3 (2021): 1057-1070, https://dx.doi.org/10.1093/plphys/kiab392.