Protein localisation in a divergent eukaryotic parasite

© 2013 Dr. Benjamin James WoodcroftMalaria infects 200 million people every year, with more than half a million of those cases resulting in death. Understanding the cell biology of Plasmodium falciparum remains largely an unsolved and unexplored problem. This doctoral assertion furthers understanding by investigating the sub-cellular localisation of Plasmodium falciparum proteins. A comprehensive literature review was undertaken, and the sub-cellular localisations of hundreds of proteins has been recorded in a transparent, traceable, publicly accessible and tactile fashion, and this serves as the basis for the further studies undertaken. It has been named ApiLoc. Using this curated set of protein localisations, the first Plasmodium falciparum-specific algorithm to predict sub-cellular localisation globally was created. Amino-acid based protein features were useful for prediction, but the predictor leveraged other predictive data types, such as microarray information and evolutionary conservation of the protein. Predictions were rigorously validated using both computational and epitope tagging approaches. ApiLoc also served as the basis for studies into the evolutionary conservation of protein localisation itself. This showed a remarkable lack of conservation, with only ~50% of protein localisations conserved across Apicomplexa, and ~20% throughout Eukaryota. The nucleus was studied in particular detail, given my involvement in a project to analyse isolated nuclei using a proteomic approach. Biochemical and bioinformatic studies were undertaken, providing further evidence that a classical nuclear import system involving basic-rich nuclear localisation signals is functional in Plasmodium falciparum and the evolutionarily related parasite Toxoplasma gondii