Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)
Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)
复制标题
DOI：
10.1099/ijs.0.001792-0
复制
发表时间：
2009-02-01
影响因子：
2.8
通讯作者：
Gao, Beile
中科院分区：
文献类型：
--
作者：
Gupta, Radhey S.;Gao, Beile
梭状芽胞杆菌属的物种由非常异质的细菌组合组成，它们不形成系统发育上连贯的群体。先前有人提出，只有在 16S rRNA 树中形成独特簇（簇 1）的梭状芽胞杆菌属物种的子集才应被视为梭菌属的真正代表（即，Clostridium sensu stricto）。然而，该簇目前仅以系统发育术语进行定义，并且不知道该簇中的物种独有的生化、分子或表型特征。我们在此报告基于梭菌基因组测序的系统发育和比较分析，试图弥合这一差距并阐明梭菌物种之间的进化关系。在基于 37 个高度保守蛋白的串联序列的梭状芽胞杆菌物种的系统发育树中，梭状芽胞杆菌簇 I 的物种形成了一个强有力的支持分支，通过一个长分支与所有其他梭状芽胞杆菌分开。不属于该簇的其他几种梭菌属物种与其他梭菌属物种可靠地分组在许多解析良好的进化枝中。我们的比较基因组分析发现，三个高度保守的蛋白质（DNA 旋转酶 A 中的 4 个氨基酸插入、ATIP 合酶 β 亚基中的 1 个氨基酸缺失和核糖体蛋白 S2 中的 1 个氨基酸插入）中存在 3 个保守的插入缺失，这些插入缺失是梭菌簇 I 物种所独有的，在任何其他细菌中都没有发现。对破伤风梭菌 E88 和产气荚膜梭菌 SM101 基因组中的各种蛋白质进行 BLASTP 搜索，还鉴定了 10 多种在 I 簇物种中独特发现的蛋白质。这些结果证明梭菌簇 I 的物种不仅在系统发育上不同，而且具有许多独特的分子特征。这些新发现的分子标记提供了有用的工具，以更明确的术语定义和界定严格梭状芽胞杆菌属。我们还鉴定了磷酸甘油酸脱氢酶中的 7-9 个氨基酸保守插入片段，该插入片段在热纤梭菌、伪乙醇嗜热厌氧杆菌、tengcogensis 嗜热厌氧杆菌和解糖热解纤维素同源物中独特存在，并且在所有其他细菌中都不存在。这些物种在系统发育树中形成了明确的分支，并且该插入缺失为该梭菌簇提供了潜在的分子标记。
The species of Clostridium comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of Clostridium that form a distinct cluster in the 16S rRNA tree (cluster 1) should be regarded as the true representatives of the genus Clostridium (i,e, Clostridium sensu stricto). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of Clostridium cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other Clostridium species that are not part of this cluster grouped reliably with other species of clostridia in a number of well-resolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATIP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of Clostridium cluster I and are not found in any other bacteria. BLASTP searches on various proteins in the genomes of Clostridium tetani E88 and Clostridium perfringens SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of Clostridium cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus Clostridium sensu stricto in more definitive terms. We have also identified a 7-9 aa conserved insert in the enzyme phosphoglycerate dehydrogenase that is uniquely found in the Clostridium thermocellum, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter tengcogensis and Caldicellulosiruptor saccharolyticus homologues, and is absent from all other bacteria. These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster.