Yan Shaomin, Wu Guang
State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
World J Microbiol Biotechnol. 2016 Feb;32(2):24. doi: 10.1007/s11274-015-1979-y. Epub 2016 Jan 8.
Amylase is one of the earliest characterized enzymes and has many applications in clinical and industrial settings. In biotechnological industries, the amylase activity is enhanced through modifying amylase structure and through cloning and expressing targeted amylases in different species. It is important to understand how engineered amylases can survive from generation to generation. This study used phylogenetic and statistical approaches to explore general patterns of amylases evolution, including 3118 α-amylases and 280 β-amylases from archaea, eukaryota and bacteria with fully documented taxonomic lineage. First, the phylogenetic tree was created to analyze the evolution of amylases with focus on individual amylases used in biofuel industry. Second, the average pairwise p-distance was computed for each kingdom, phylum, class, order, family and genus, and its diversity implies multi-time and multi-clan evolution. Finally, the variance was further partitioned into inter-clan variance and intra-clan variance for each taxonomic group, and they represent horizontal and vertical gene transfer. Theoretically, the results show a full picture on the evolution of amylases in manners of vertical and horizontal gene transfer, and multi-time and multi-clan evolution as well. Practically, this study provides the information on the surviving chance of desired amylase in a given taxonomic group, which may potentially enhance the successful rate of cloning and expression of amylase gene in different species.
淀粉酶是最早被鉴定的酶之一，在临床和工业领域有许多应用。在生物技术产业中，通过修饰淀粉酶结构以及在不同物种中克隆和表达目标淀粉酶来提高淀粉酶活性。了解工程化淀粉酶如何代代相传很重要。本研究采用系统发育和统计方法来探索淀粉酶进化的一般模式，包括来自古菌、真核生物和细菌的3118种α-淀粉酶和280种β-淀粉酶，其分类谱系有完整记录。首先，构建系统发育树以分析淀粉酶的进化，重点关注生物燃料工业中使用的个别淀粉酶。其次，计算每个界、门、纲、目、科和属的平均成对p距离，其多样性意味着多次和多谱系进化。最后，将每个分类组的方差进一步划分为谱系间方差和谱系内方差，它们分别代表水平和垂直基因转移。理论上，结果从垂直和水平基因转移以及多次和多谱系进化的角度全面展示了淀粉酶的进化情况。实际上，本研究提供了给定分类组中所需淀粉酶存活机会的信息，这可能会提高淀粉酶基因在不同物种中克隆和表达的成功率。
