Wang Boqian, Jin Yuan, Hu Mingda, Zhao Yunxiang, Wang Xin, Yue Junjie, Ren Hongguang
Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China.
Heliyon. 2024 May 31;10(11):e32103. doi: 10.1016/j.heliyon.2024.e32103. eCollection 2024 Jun 15.
Continuous gain and loss of genes are the primary driving forces of bacterial evolution and environmental adaptation. Studying bacterial evolution in terms of protein domain, which is the fundamental function and evolutionary unit of proteins, can provide a more comprehensive understanding of bacterial differentiation and phenotypic adaptation processes. Therefore, we proposed a phylogenetic tree-based method for detecting genetic gain and loss events in terms of protein domains. Specifically, the method focuses on a single domain to trace its evolution process or on multiple domains to investigate their co-evolution principles. This novel method was validated using 122 isolates. We found that the loss of a significant number of domains was likely the main driving force behind the evolution of , which could reduce energy expenditure and preserve only the most essential functions. Additionally, we observed that simultaneously gained and lost domains were often functionally related, which can facilitate and accelerate phenotypic evolutionary adaptation to the environment. All results obtained using our method agree with those of previous studies, which validates our proposed method.
基因的持续获得与丢失是细菌进化和环境适应的主要驱动力。从蛋白质结构域的角度研究细菌进化，蛋白质结构域是蛋白质的基本功能和进化单位，能够更全面地理解细菌分化和表型适应过程。因此，我们提出了一种基于系统发育树的方法来检测蛋白质结构域层面的基因获得与丢失事件。具体而言，该方法聚焦于单个结构域以追踪其进化过程，或聚焦于多个结构域以研究它们的共同进化原理。使用122个分离株对这种新方法进行了验证。我们发现大量结构域的丢失可能是[此处原文缺失具体物种名称]进化背后的主要驱动力，这可以减少能量消耗并仅保留最基本的功能。此外，我们观察到同时获得和丢失的结构域通常在功能上相关，这能够促进和加速对环境的表型进化适应。使用我们的方法获得的所有结果与先前研究的结果一致，这验证了我们提出的方法。
