Parasite Genetics and Adaption - Project B1
RNA Processing and turnover in Apicomplexan organelles
Host labs: C. Schmitz-Linneweber, Molecular Genetics at Humboldt University Berlin; Melanie Rug, Alex Maier, ANU Canberra
Partner labs: Kai Matuschewski, HU Berlin: P. berghei genetics; Frank Seeber, RKI Berlin: T. gondii genetics, Melanie Rug, ANU Canberra: cryoelectron tomography
Background: Apicoplasts and mitochondria contain their own genetic information. Gene expression in these organelles is essential for parasite survival. Antibiotics targeting gene expression in the apicoplast and mitochondrion serve as potent antimalarials. Very little is known about the organellar gene expression machinery in Apicomplexans. We recently identified a family of RNA binding proteins named heptatricopeptide repeat proteins (HPR proteins; Hillebrand et al., 2018). Members of this family were demonstrated to reside in RNA granules in human mitochondria (Jourdain et al., 2017) and play a role in rRNA and mRNA processing. Initial gene tagging and knock-out approaches demonstrated that these proteins reside in mitochondria and are essential for parasite survival. Their exact functions in mitochondrial RNA metabolism remains enigmatic. In general, RNA turnover and its regulation is hardly addressed in Apicomplexans, neither in organelles nor in the nucleo-cytoplasmic compartment. This project aims at filling this gap in our knowledge.
Central Question: What is the role of Apicomplexan HPR proteins in RNA processing and stabilization?
Outline of 3-year plan:
Year 1: Berlin. Preparation of tagged lines, knock-out mutants, and inducible mutants of HPR proteins. Mutant analysis using RNA Seq, ERIC-Seq and Nanopore sequencing.
Year 2: Canberra. Search for interaction partners of HPR proteins using proximity labelling. Analysis of the localization of HPR proteins using cryo-lectron tomography
Year 3: Berlin. CLIP-Seq of selected HPR proteins. STED microscopy of HPR proteins and RNA granules. Writing up thesis.
Keywords: Mitochondria, RNA processing and turnover, HPR proteins
Reference: Hillebrand, A., Matz, J.M., Almendinger, M., Muller, K., Matuschewski, K., and Schmitz-Linneweber, C. (2018). Identification of clustered organellar short (cos) RNAs and of a conserved family of organellar RNA-binding proteins, the heptatricopeptide repeat proteins, in the malaria parasite. Nucleic Acids Res. 46(19):10417-10431. doi: 10.1093/nar/gky710.
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