Comparative systems biology of apicomplexan cell division

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Summary Apicomplexan parasites have major impacts on human health e.g. Plasmodium falciparum causes malaria whereas Toxoplasma gondii and Babesia spp. cause opportunistic infections. Although this close-knit group shares their obligate intracellular life styles, they display a wide variety of asexual cell division modes. These differ between parasites as well as between different life stages within a single parasite species, but the start- and end-point is always a host cell invasion competent ‘zoite’. The number of zoites made per division round varies dramatically (from 2-90,000) and can unfold in several different ways by reshuffling the functional modules of 1) mother cytoskeleton disassembly, 2) DNA synthesis and chromosome segregation (D&S), 3) karyokinesis, and 4) zoite assembly (budding). Distinct cell division modes across Apicomplexa arise from variations in the order and sequence of the modules as well as the number of module repetitions. In the current model, cell division progresses in transcriptional waves mediated transcription factors that act on target genes that in turn bundle into the functional modules. However, little is known of the composition, regulators and wiring of the different modules, and how this leads to the diversity of cell division modes in Apicomplexa. The research team hypothesizes that these questions can be answered by a comparative systems biology approach, starting with parasites representing different diverse and ‘exotic’ division cell division modes wherein particular modules are amplified, or combined differently: Babesia divergens binary fission, P. falciparum schizogony, Sarcocystis neurona endopolygeny without karyokinesis, T. gondii asexual endodyogeny and T. gondii pre-sexual endopolygeny with karyokinesis in the definitive host. This approach takes advantage of the single cell sequencing revolution combined with computational network analysis approaches. Firstly, single cell transcriptomic and epigenomic maps of the five cell division modes will be generated and analyzed to define the effectors contained in each specific module. A subset of uncharacterized effectors in the poorly characterized karyokinesis and cytoskeleton disassembly modules will be experimentally validated by gene knock-downs. Secondly, chemical and genetic perturbations combined with single cell sequencing will enable the assembly of causal gene regulatory networks (GRNs) across all division modes. Candidate module controllers in these GRNs will be validated by reprogramming and/or genetic perturbation experiments: changing (parts of) the division mode in specific parasites. This work will answer elusive questions regarding apicomplexan specific biology within barely studied functional modules, as well as how apicomplexan cell division flexibility is wired. Thirdly, the proposed work will produce extensive community resources comprising single expression and chromatin accessibility atlases across five different cell division modes and parasite species. Moreover, data sets will be searchable across systems in real time for any biological feature of interest by web-based Apps that will be incorporated in VEuPathDB and enable querying the data for biological questions beyond cell division.