Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection.
Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection.
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通过水平基因转移和正选择编码 L-Ala-D/L-Glu 差向异构酶 (AEE) 的陆地植物基因的进化
DOI：
10.1186/1471-2229-13-34
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发表时间：
2013-03-01
影响因子：
5.3
通讯作者：
Xu C
中科院分区：
文献类型：
--
作者：
Yang Z;Wang Y;Zhou Y;Gao Q;Zhang E;Zhu L;Hu Y;Xu C
背景L-Ala-D/L-Glu差向异构酶（AEEs）是烯醇化酶超家族的一个亚类，在细菌中催化L-Ala-D/L-Glu等二肽的差向异构化，并参与肽聚糖中胞壁肽的代谢。虽然缺乏肽聚糖，陆地植物possessAEE基因，表现出高度的相似性，在bacteries.ResultsSimilarity搜索显示，theAEE基因是无处不在的陆地植物，从被子植物的brandetas。然而，其他真核生物，包括绿色和红藻，不包含编码具有L-Ala-D/L-Glu_差向异构酶结构域的蛋白质的基因。陆生植物AEE基因的同源物仅存在于原核生物中，尤其是细菌中。系统发育分析表明，陆生植物AEE基因与一些细菌同源物形成了一个单系群。此外，陆地植物AEE蛋白与这些细菌同源物的相似性最高，并且具有陆地植物和这些细菌AEE中唯一保守的基序。综合AEE蛋白的分类分布、系统发育关系和序列相似性等信息，揭示陆生植物AEE基因是通过古老的水平基因转移（HGT）事件从细菌中获得的。进一步的证据表明，陆生植物AEE基因在陆生植物祖先的进化过程中经历了正向选择，并通过获得一些内含子而形成了其外显子/内含子结构的主要特征。其他研究结果表明，通过积极选择的适应性进化有助于该基因在陆地植物中的功能适应和固定。
BackgroundThe L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan. Although lacking in peptidoglycan, land plants possessAEEgenes that show high similarity to those in bacteria.ResultsSimilarity searches revealed that theAEEgene is ubiquitous in land plants, from bryophytas to angiosperms. However, other eukaryotes, including green and red algae, do not contain genes encoding proteins with an L-Ala-D/L-Glu_epimerase domain. Homologs of land plantAEEgenes were found to only be present in prokaryotes, especially in bacteria. Phylogenetic analysis revealed that the land plantAEEgenes formed a monophyletic group with some bacterial homologs. In addition, land plant AEE proteins showed the highest similarity with these bacterial homologs and shared motifs only conserved in land plant and these bacterial AEEs. Integrated information on the taxonomic distribution, phylogenetic relationships and sequence similarity of the AEE proteins revealed that the land plantAEEgenes were acquired from bacteria through an ancient horizontal gene transfer (HGT) event. Further evidence revealed that land plantAEEgenes had undergone positive selection and formed the main characteristics of exon/intron structures through gaining some introns during the initially evolutionary period in the ancestor of land plants.ConclusionsThe results of this study clearly demonstrated that the ancestor of land plants acquired anAEEgene from bacteria via an ancient HGT event. Other findings illustrated that adaptive evolution through positive selection has contributed to the functional adaptation and fixation of this gene in land plants.
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DOI：
10.1016/j.str.2008.08.015
发表时间：
2008-11-12
期刊：
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影响因子：
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作者：
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