Peregrín-Alvarez José M, Xiong Xuejian, Su Chong, Parkinson John
Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.
PLoS Comput Biol. 2009 Oct;5(10):e1000523. doi: 10.1371/journal.pcbi.1000523. Epub 2009 Oct 2.
Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks.
大肠杆菌是研究诸如新陈代谢、信号传导和基因表达等基本细胞过程的优秀模型。了解这些过程中蛋白质的功能和组织是迈向大肠杆菌“系统”观点的重要一步。整合实验和计算相互作用数据，我们展示了一个由1941种大肠杆菌蛋白质（约占其蛋白质组的45%）之间的3989种功能相互作用组成的可靠网络。这些相互作用与最近生成的一组918种蛋白质之间的3888种高质量物理相互作用相结合，并进行聚类以揭示316个离散模块。除了已知的蛋白质复合物（如RNA和DNA聚合酶）外，我们还鉴定出代表生化途径（如硝酸盐调节和细胞壁生物合成）以及功能和进化相关过程组的模块。为了帮助解释模块关系，我们给出了几个案例，包括特征明确的和新的生化系统。这些数据共同提供了大肠杆菌蛋白质组模块化组织的全局视图，并对细菌网络中的结构和进化关系产生了独特的见解。
