An investigation into the role and mechanism of action of small ubiquitin-like modifier interacting motifs in Arabidopsis thaliana proteins

• Main Author: Nelis, Stuart
• Format: Dissertation
• Language: English
• Published: University of Warwick 2014
• Subjects: QH301 Biology

SUMO is a small protein that is ligated to other proteins to regulate their function. Ligation occurs at lysine residues within a SUMO site motif. A wide range of proteins are targets of SUMOylation and in plants SUMO plays a diverse role in many important processes. Processes including development, stress tolerance, hormone regulation, DNA repair and chromatin remodelling are regulated by SUMOylation. SUMO affects protein function primarily by establishing interactions through SUMO interacting motifs (SIMs) in interacting protein partners. SUMO can also alter protein function by blocking access to protein domains and by causing conformational changes to the target. The ability to predict SIMs in plant proteins would be useful for research into the poorly understood mechanisms behind SUMO regulation. Large arrays of synthetic peptides were screened with SUMO to identify SIM peptides. These data were used to characterise the sequence composition of plant SIMs. The plant SIMs were compared and contrasted with human SIMs to highlight the functional differences between these two evolutionary distinct species. The data were used to build a predictor for SIMs using random forest models. A new SUMO site predictor was built using random forest models as well. The SIM predictor was used to identify putative SIM containing proteins in the Arabidopsis thaliana genome and the functional enrichment of these genes was analysed. The role of SUMO in the plant gibberellin (GA) pathway was also investigated. The DELLA protein RGA is a negative regulator of GA signalling and this protein was shown to be SUMOylated. RGA stability is regulated by the GA receptor GID1 and it was demonstrated that GID1a contains a SIM. It was proposed that SUMOylated RGA interacted with GID1a through its SIM which inhibited its function. The model was tested by investigating the binding of SUMO to GID1a and by generating mutants of GID1a that had reduced SUMO a affinity. The results demonstrate that GA signalling can be enhanced by introducing a mutation into the GID1a SIM.