Pasek Sophie, Risler Jean-Loup, Brézellec Pierre
Laboratoire Statistique et Génome 523 Place des Terrasses, 91034 Evry cedex, France.
Bioinformatics. 2006 Jun 15;22(12):1418-23. doi: 10.1093/bioinformatics/btl135. Epub 2006 Apr 6.
Most proteins comprise one or several domains. New domain architectures can be created by combining previously existing domains. The elementary events that create new domain architectures may be categorized into three classes, namely domain(s) insertion or deletion (indel), exchange and repetition. Using 'DomainTeam', a tool dedicated to the search for microsyntenies of domains, we quantified the relative contribution of these events. This tool allowed us to collect homologous bacterial genes encoding proteins that have obviously evolved by modular assembly of domains. We show that indels are the most frequent elementary events and that they occur in most cases at either the N- or C-terminus of the proteins. As revealed by the genomic neighbourhood/context of the corresponding genes, we show that a substantial number of these terminal indels are the consequence of gene fusions/fissions. We provide evidence showing that the contribution of gene fusion/fission to the evolution of multi-domain bacterial proteins is lower-bounded by 27% and upper-bounded by 64%. We conclude that gene fusion/fission is a major contributor to the evolution of multi-domain bacterial proteins.
大多数蛋白质由一个或多个结构域组成。新的结构域架构可通过组合先前存在的结构域来创建。产生新结构域架构的基本事件可分为三类，即结构域插入或缺失（indel）、交换和重复。我们使用“DomainTeam”（一种专门用于搜索结构域微共线性的工具）来量化这些事件的相对贡献。该工具使我们能够收集编码通过结构域模块化组装明显进化而来的蛋白质的同源细菌基因。我们表明，插入缺失是最常见的基本事件，并且在大多数情况下它们发生在蛋白质的N端或C端。正如相应基因的基因组邻域/背景所揭示的那样，我们表明这些末端插入缺失中有相当一部分是基因融合/裂变的结果。我们提供的证据表明，基因融合/裂变对多结构域细菌蛋白质进化的贡献下限为27%，上限为64%。我们得出结论，基因融合/裂变是多结构域细菌蛋白质进化的主要贡献因素。
