The Binary Protein Interactome of Treponema pallidum �C The Syphilis Spirochete

Protein interaction networks shed light on the global organization of proteomes but can also place individual proteins into a functional context. If we know the function of bacterial proteins we will be able to understand how these species have adapted to diverse environments including many extreme habitats. Here we present the protein interaction network for the syphilis spirochete Treponema pallidum which encodes 1,039 proteins, 726 (or 70%) of which interact via 3,649 interactions as revealed by systematic yeast two-hybrid screens. A high-confidence subset of 991 interactions links 576 proteins. To derive further biological insights from our data, we constructed an integrated network of proteins involved in DNA metabolism. Combining our data with additional evidences, we provide improved annotations for at least 18 proteins (including TP0004, TP0050, and TP0183 which are suggested to be involved in DNA metabolism). We estimate that this ��minimal�� bacterium contains on the order of 3,000 protein interactions. Profiles of functional interconnections indicate that bacterial proteins interact more promiscuously than eukaryotic proteins, reflecting the non-compartmentalized structure of the bacterial cell. Using our high-confidence interactions, we also predict 417,329 homologous interactions (��interologs��) for 372 completely sequenced genomes and provide evidence that at least one third of them can be experimentally confirmed.

蛋白质互作网络（Protein interaction networks）不仅能够揭示蛋白质组（proteome）的全局组织模式，还可将单个蛋白质置于其功能背景中开展研究。若明确细菌蛋白质的功能，我们便能理解这些物种如何适应包括诸多极端生境在内的多样环境。本研究构建了梅毒螺旋体（Treponema pallidum）的蛋白质互作网络：该致病菌编码1039个蛋白质，其中726个（占比70%）通过3649次互作发生关联，该结果由系统性酵母双杂交筛选实验所得。其中991次互作构成高置信度互作子集，关联了576个蛋白质。为从本研究数据中获取更多生物学洞见，我们构建了参与DNA代谢（DNA metabolism）的蛋白质整合互作网络。结合本研究数据与其他佐证证据，我们为至少18个蛋白质提供了优化后的功能注释，其中包括TP0004、TP0050与TP0183，这三个蛋白质被推测参与DNA代谢过程。我们估算，这一"极简"细菌的蛋白质互作数量约为3000次。功能互作图谱显示，细菌蛋白质的互作广谱性高于真核蛋白质，这反映了细菌细胞无区室化的结构特征。基于本研究的高置信度互作数据，我们还为372个已完成全基因组测序的物种预测了417329次同源互作（interologs），并证实其中至少三分之一可通过实验验证。