Comparative systems biology of apicomplexan cell division

摘要 Apicomplexan寄生虫对人类健康有重大影响，例如恶性疟原虫导致疟疾 弓形虫和巴贝斯虫。引起机会性感染。尽管这个关系密切的团体 它们共有专属的细胞内生活方式，表现出各种各样的无性细胞分裂模式。这些 寄生虫之间以及同一寄生虫物种内不同生命阶段之间的差异，但开始- 而终点始终是宿主细胞入侵能力强的‘Zite’。每一轮分区产生的动物数量 变化很大(从2到90,000)，并可以通过重新洗牌功能模块以几种不同的方式展开 1)母细胞骨架解体，2)DNA合成和染色体分离(D&S)，3)核分裂， (4)带状集合体(萌发)。顶层复合体上不同的细胞分裂模式源于 模块的顺序和顺序以及模块重复的次数。在当前模型中，单元 转录波介导的转录因子作用于靶基因，进而作用于靶基因 捆绑到功能模块中。然而，人们对其组成、调节器和接线知之甚少 不同的模块，以及这如何导致Apicomplexa中细胞分裂模式的多样性。研究团队 假设这些问题可以通过比较系统生物学的方法来回答，从 代表不同的不同的和“外来的”分裂细胞分裂模式的寄生虫，其中特定的模块是 扩增，或以不同方式组合：巴贝斯虫二次分裂，恶性疟原虫分裂，肉孢子虫 无核分裂的神经元内生、弓形虫无性内生和性前弓形虫 在最终宿主中有核分裂的内源多聚体。这种方法利用了单个单元的优势 排序革命与计算网络分析相结合的方法。首先，单细胞 将生成并分析五种细胞分裂模式的转录和表观基因组图，以定义 每个特定模块中包含的效应器。未角色化的效应器的子集 核分裂和细胞骨架分解模块将通过基因敲除进行实验验证。 其次，化学和遗传干扰与单细胞测序相结合将使组装 跨所有分裂模式的因果基因调控网络(GRN)。这些GRN中的候选模块控制器 将通过重新编程和/或遗传扰动实验来验证：改变(部分)除法 在特定寄生虫中的模式。这项工作将回答有关apicplexan特定生物学的难以捉摸的问题。 在鲜有研究的功能模块中，以及顶端复合体细胞分裂的灵活性是如何连接的。第三， 拟议的工作将产生广泛的社区资源，包括单一表达和染色质 五种不同细胞分裂模式和寄生虫物种的可及性图谱。此外，数据集将被 基于Web的应用程序可跨系统实时搜索感兴趣的任何生物特征，这些应用程序将 整合在VEuPathDB中，并支持查询细胞分裂以外的生物问题的数据。

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.