Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling.
Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling.
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DOI：
10.1074/mcp.m110.004119
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发表时间：
2010-12
期刊：
影响因子：
--
通讯作者：
Wright GJ
中科院分区：
文献类型：
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作者：
Martin S;Söllner C;Charoensawan V;Adryan B;Thisse B;Thisse C;Teichmann S;Wright GJ
涉及分泌型和膜系受体蛋白的细胞外相互作用对于启动在生物系统内协调细胞行为的信号传导途径是必不可少的。由于这些蛋白质及其相互作用的生物化学性质，确定新的细胞外相互作用仍然具有实验挑战性。为了解决这个问题，我们最近开发了一种检测方法，AVEXIS（亲合力为基础的细胞外相互作用屏幕），以检测低亲和力的细胞外相互作用在大规模上，并已开始构建属于免疫球蛋白和富含亮氨酸的重复蛋白家族的斑马鱼受体之间的相互作用网络，以确定新的信号通路的重要早期发展。在这里，我们扩展了我们的斑马鱼蛋白库，包括其他结构域家族和更多的分泌蛋白，并进行了迄今为止最大的筛选，总计16，544种潜在的独特相互作用。我们报告了111种相互作用，其中96种是新的，包括第一个记录的15种蛋白质的细胞外配体。通过包括来自先前筛选的77种相互作用，我们组装了92种蛋白质之间的188种细胞外相互作用的扩展网络，并使用它来显示分泌蛋白质的相互作用伴侣是膜系受体的两倍，并且细胞外网络的连接性表现为幂律。为了试图了解这些相互作用的功能作用，我们确定了新的表达模式，在我们的克隆库中的164个基因，在斑马鱼胚胎发育的五个关键阶段使用全胚胎原位杂交。将这些表达数据与结合网络整合，以揭示每个相互作用可能在胚胎内发挥作用的位置，并用于将静态相互作用网络解析为发育中的斑马鱼胚胎内的动态组织和阶段特异性子网络。所有这些数据被组织到一个免费访问的在线数据库，称为ARNIE（AVEXIS受体网络与综合表达; www.sanger.ac.uk/arnie），并提供了一个有价值的资源，新的细胞外信号相互作用的发育生物学。
Extracellular interactions involving both secreted and membrane-tethered receptor proteins are essential to initiate signaling pathways that orchestrate cellular behaviors within biological systems. Because of the biochemical properties of these proteins and their interactions, identifying novel extracellular interactions remains experimentally challenging. To address this, we have recently developed an assay, AVEXIS (avidity-based extracellular interaction screen) to detect low affinity extracellular interactions on a large scale and have begun to construct interaction networks between zebrafish receptors belonging to the immunoglobulin and leucine-rich repeat protein families to identify novel signaling pathways important for early development. Here, we expanded our zebrafish protein library to include other domain families and many more secreted proteins and performed our largest screen to date totaling 16,544 potential unique interactions. We report 111 interactions of which 96 are novel and include the first documented extracellular ligands for 15 proteins. By including 77 interactions from previous screens, we assembled an expanded network of 188 extracellular interactions between 92 proteins and used it to show that secreted proteins have twice as many interaction partners as membrane-tethered receptors and that the connectivity of the extracellular network behaves as a power law. To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development. These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo. All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.