From the ‡Dept. of Computer Science.
§Center for Computational Science.
Mol Cell Proteomics. 2018 May;17(5):961-973. doi: 10.1074/mcp.RA117.000474. Epub 2018 Feb 1.
is a common pathogen that is estimated to infect half of the human population, causing several diseases such as duodenal ulcer. Despite one of the first pathogens to be sequenced, its proteome remains poorly characterized as about one-third of its proteins have no functional annotation. Here, we integrate and analyze known protein interactions with proteomic and genomic data from different sources. We find that proteins with similar abundances tend to interact. Such an observation is accompanied by a trend of interactions to appear between proteins of similar functions, although some show marked cross-talk to others. Protein function prediction with protein interactions is significantly improved when interactions from other bacteria are included in our network, allowing us to obtain putative functions of more than 300 poorly or previously uncharacterized proteins. Proteins that are critical for the topological controllability of the underlying network are significantly enriched with genes that are up-regulated in the spiral compared with the coccoid form of Determining their evolutionary conservation, we present evidence that 80 protein complexes are identical in composition with their counterparts in , while 85 are partially conserved and 120 complexes are completely absent. Furthermore, we determine network clusters that coincide with related functions, gene essentiality, genetic context, cellular localization, and gene expression in different cellular states.
是一种常见的病原体，据估计，它感染了一半的人类人口，导致多种疾病，如十二指肠溃疡。尽管它是最早被测序的病原体之一，但由于其约三分之一的蛋白质没有功能注释，因此其蛋白质组仍未得到很好的描述。在这里，我们整合并分析了来自不同来源的已知蛋白质相互作用与蛋白质组学和基因组学数据。我们发现，丰度相似的蛋白质往往相互作用。这种观察伴随着一种趋势，即功能相似的蛋白质之间会出现相互作用，尽管有些蛋白质与其他蛋白质有明显的交叉对话。当我们的网络中包含来自其他细菌的相互作用时，利用蛋白质相互作用进行蛋白质功能预测会得到显著改善，这使我们能够获得 300 多个功能不佳或以前未被描述的蛋白质的可能功能。对于底层网络拓扑可控性至关重要的蛋白质，与螺旋体相比，螺旋体中上调的基因显著富集。确定它们的进化保守性，我们提供的证据表明，80 个蛋白质复合物在组成上与 中的对应物相同，而 85 个复合物部分保守，120 个复合物完全不存在。此外，我们确定了与相关功能、基因必需性、遗传背景、细胞定位以及不同细胞状态下基因表达一致的网络簇。
