Identification and analysis of evolutionarily cohesive functional modules in protein networks
Identification and analysis of evolutionarily cohesive functional modules in protein networks
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DOI：
10.1101/gr.4336406
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发表时间：
2006-03-01
期刊：
影响因子：
7
通讯作者：
Bork, P
中科院分区：
文献类型：
--
作者：
Campillos, M;von Mering, C;Bork, P
越来越多的测序基因组使得推断功能模块的进化历史成为可能，即，在特定物种中共同贡献相同细胞功能的蛋白质组。在这里，我们确定和分析这些原核生物的功能模块，其组成在进化过程中基本保持不变，并研究其性质。这种“内聚”模块具有大量的内部功能连接，其编码基因往往在原核基因组中非常接近，并且对应于物理复合物或复杂的功能系统，如鞭毛装置。内聚模块在能量和氨基酸代谢、细胞运动和细胞内运输或分泌等过程中富集。通过将基因分组到模块中，我们实现了对它们年龄的更精确估计，并发现年轻模块通常在物种之间水平转移，并且富含与环境相互作用的功能，这意味着它们在物种适应新环境中发挥着重要作用。
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in a given species. Here we identify and analyze those prokaryotic functional modules, whose composition remains largely unchanged during evolution, and study their properties. Such "cohesive" modules have a large number of internal functional connections encode genes that tend to be in close proximity in prokaryotic genomes, and correspond to physical complexes or complex functional systems like the flagellar apparatus. Cohesive modules are enriched in processes such as energy and amino acid metabolism, cell motility, and intracellular trafficking, or secretion. By grouping genes into modules we achieve a more precise estimate of their age and find that the young modules are often horizontally transferred between species and are enriched in functions involved in interactions with the environment, implying that they play an important role in the adaptation of species to new environments.