CLK1/CLK2-driven signalling at the Leishmania kinetochore is captured by spatially referenced proximity phosphoproteomics

• Published in: Communications biology 2022-11, Vol.5 (1), p.1305-1305, Article 1305
• Main Authors: Geoghegan, Vincent, Carnielli, Juliana B. T., Jones, Nathaniel G., Saldivia, Manuel, Antoniou, Sergios, Hughes, Charlotte, Neish, Rachel, Dowle, Adam, Mottram, Jeremy C.
• Format: Article
• Language: English
• Subjects: 631/326/417/1716; 631/45/275; 82; 82/58; Biology; Biomedical and Life Sciences; Biotin; Biotinylation; Cell cycle; Cytokinesis; Enzyme inhibitors; Kinases; Kinetochores; Labeling; Leishmania; Life Sciences; Parasites; Protein Kinase Inhibitors; Proteins; Signal transduction; Therapeutic targets
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-022-04280-1

Kinetochores in the parasite Leishmania and related kinetoplastids appear to be unique amongst eukaryotes and contain protein kinases as core components. Using the kinetochore kinases KKT2, KKT3 and CLK2 as baits, we developed a BirA* proximity biotinylation methodology optimised for sensitivity, XL-BioID, to investigate the composition and function of the Leishmania kinetochore. We could detect many of the predicted components and also discovered two novel kinetochore proteins, KKT24 and KKT26. Using KKT3 tagged with a fast-acting promiscuous biotin ligase variant, we took proximity biotinylation snapshots of the kinetochore in synchronised parasites. To quantify proximal phosphosites at the kinetochore as the parasite progressed through the cell cycle, we further developed a spatially referenced proximity phosphoproteomics approach. This revealed a group of phosphosites at the kinetochore that were highly dynamic during kinetochore assembly. We show that the kinase inhibitor AB1 targets CLK1/CLK2 (KKT10/KKT19) in Leishmania leading to defective cytokinesis. Using AB1 to uncover CLK1/CLK2 driven signalling pathways important for kinetochore function at G2/M, we found a set of 16 inhibitor responsive kinetochore-proximal phosphosites. Our results exploit new proximity labelling approaches to provide a direct analysis of the Leishmania kinetochore, which is emerging as a promising drug target. Combination of proximity biotinylation and protein cross-linking allows proximity phosphoproteomics of the kinetochore in Leishmania parasites during the cell cycle and captures perturbations at the kinetochore after treatment with a protein kinase inhibitor.