Phylogenetic analysis of the triterpene cyclase protein family in prokaryotes and eukaryotes suggests bidirectional lateral gene transfer
Phylogenetic analysis of the triterpene cyclase protein family in prokaryotes and eukaryotes suggests bidirectional lateral gene transfer
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DOI：
10.1111/j.1462-2920.2008.01851.x
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发表时间：
2009-05-01
影响因子：
5.1
通讯作者：
Kannenberg, Elmar
中科院分区：
文献类型：
--
作者：
Frickey, Tancred;Kannenberg, Elmar
三萜环化酶氨基酸序列的功能限制，使它们成为很好的候选人，这些酶在原核生物以及真核生物中的系统发育相关性的进化研究。在这项研究中，我们使用了一组确定的三萜环化酶，一组主要是细菌角鲨烯环化酶和一组主要是真核氧化角鲨烯环化酶，作为种子序列，以确定5288推定的三萜环化酶同源物在公开可用的数据库。使用序列聚类分析软件检测具有增加的成对序列相似性的序列组。序列分为两个主要的集群，细菌和真核生物。使用AsaturA和最大似然系统发育树，使用PhyML软件的家庭的多序列比对的保守的，信息丰富的区域被用来构建相邻连接的系统发育树。这两个分析表明，大多数的三萜环化酶序列类似地分组的生物体的公认的分类学关系的序列起源，支持环化酶基因从父母到后代的垂直转移的想法，在这个蛋白质家族的主要进化驱动力。然而，一小组的序列从三个细菌物种（柱头菌，芽和甲基球菌）分组，否则纯真核簇的氧化角鲨烯环化酶，而一小组的序列从七个真菌物种和一个序列从蕨类铁线蕨分组一致，否则纯细菌的角鲨烯环化酶的簇。这表明，横向基因转移可能已经发生，需要转移氧化角鲨烯环化酶从真核生物的细菌和角鲨烯环化酶从细菌的Pezizomycotina真菌组的祖先。
Functional constraints to modifications in triterpene cyclase amino acid sequences make them good candidates for evolutionary studies on the phylogenetic relatedness of these enzymes in prokaryotes as well as in eukaryotes. In this study, we used a set of identified triterpene cyclases, a group of mainly bacterial squalene cyclases and a group of predominantly eukaryotic oxidosqualene cyclases, as seed sequences to identify 5288 putative triterpene cyclase homologues in publicly available databases. The Cluster Analysis of Sequences software was used to detect groups of sequences with increased pairwise sequence similarity. The sequences fall into two main clusters, a bacterial and a eukaryotic. The conserved, informative regions of a multiple sequence alignment of the family were used to construct a neighbour-joining phylogenetic tree using the AsaturA and maximum likelihood phylogenetic tree using the PhyML software. Both analyses showed that most of the triterpene cyclase sequences were similarly grouped to the accepted taxonomic relationships of the organism the sequences originated from, supporting the idea of vertical transfer of cyclase genes from parent to offspring as the main evolutionary driving force in this protein family. However, a small group of sequences from three bacterial species (Stigmatella, Gemmata and Methylococcus) grouped with an otherwise purely eukaryotic cluster of oxidosqualene cyclases, while a small group of sequences from seven fungal species and a sequence from the fern Adiantum grouped consistently with a cluster of otherwise purely bacterial squalene cyclases. This suggests that lateral gene transfer may have taken place, entailing a transfer of oxidosqualene cyclases from eukaryotes to bacteria and a transfer of squalene cyclase from bacteria to an ancestor of the group of Pezizomycotina fungi.