Wang Xiu, Jin Yongfeng
Institute of Ecology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China.
Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China.
BMC Genomics. 2017 Sep 11;18(1):716. doi: 10.1186/s12864-017-4085-8.
Stegodyphus mimosarum is a candidate model organism belonging to the class Arachnida in the phylum Arthropoda. Studies on the biology of S. mimosarum over the past several decades have consisted of behavioral research and comparison of gene sequences based on the assembled genome sequence. Given the lack of systematic protein analyses and the rich source of information in the genome, we predicted the relationships of proteins in S. mimosarum by bioinformatics comparison with genome-wide proteins from select model organisms using gene mapping.
The protein-protein interactions (PPIs) of 11 organisms were integrated from four databases (BioGrid, InAct, MINT, and DIP). Here, we present comprehensive prediction and analysis of 3810 proteins in S. mimosarum with regard to interactions between proteins using PPI data of organisms. Interestingly, a portion of the protein interactions conserved among Saccharomyces cerevisiae, Homo sapiens, Arabidopsis thaliana, and Drosophila melanogaster were found to be associated with RNA splicing. In addition, overlap of predicted PPIs in reference organisms, Gene Ontology, and topology models in S. mimosarum are also reported.
Addition of Stegodyphus, a spider representative of interactomic research, provides the possibility of obtaining deeper insights into the evolution of PPI networks among different animal species. This work largely supports the utility of the "stratus clouds" model for predicted PPIs, providing a roadmap for integrative systems biology in S. mimosarum.
猛蛛（Stegodyphus mimosarum）是节肢动物门蛛形纲的一种候选模式生物。在过去几十年里，对猛蛛生物学的研究包括行为研究以及基于组装后的基因组序列进行的基因序列比较。鉴于缺乏系统的蛋白质分析且基因组中有丰富的信息来源，我们通过基因定位，将猛蛛的蛋白质与选定模式生物的全基因组蛋白质进行生物信息学比较，从而预测猛蛛中蛋白质之间的关系。
从四个数据库（BioGrid、InAct、MINT和DIP）整合了11种生物的蛋白质 - 蛋白质相互作用（PPI）数据。在此，我们利用生物的PPI数据，对猛蛛中的3810种蛋白质之间的相互作用进行了全面的预测和分析。有趣的是，发现酿酒酵母、人类、拟南芥和黑腹果蝇之间保守的一部分蛋白质相互作用与RNA剪接有关。此外，还报告了参考生物中预测的PPI、基因本体以及猛蛛中的拓扑模型的重叠情况。
添加猛蛛这种蛋白质相互作用组学研究的蜘蛛代表，为更深入了解不同动物物种间PPI网络的进化提供了可能。这项工作在很大程度上支持了“层云”模型用于预测PPI的实用性，为猛蛛的综合系统生物学提供了路线图。
