Gupta Radhey S, Gao Beile
Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
Int J Syst Evol Microbiol. 2009 Feb;59(Pt 2):285-94. doi: 10.1099/ijs.0.001792-0.
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 I) 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 ATP 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.
梭菌属的细菌种类非常多样，它们并非构成一个系统发育上连贯的群体。此前有人提出，只有在16S rRNA树中形成一个独特簇（簇I）的梭菌属物种的一个子集才应被视为梭菌属的真正代表（即狭义梭菌属）。然而，目前这个簇仅从系统发育角度进行定义，还没有已知的生化、分子或表型特征是该簇物种所独有的。我们在此报告基于已测序的梭菌基因组进行的系统基因组学和比较分析，试图弥合这一差距，并阐明梭菌属物种之间的进化关系。在基于37种高度保守蛋白质的串联序列构建的梭菌属物种的系统发育树中，梭菌属簇I的物种形成了一个得到有力支持的进化枝，它通过一个长分支与所有其他梭菌分开。其他一些不属于这个簇的梭菌物种在一些解析良好的进化枝中与其他梭菌物种可靠地聚在一起。我们的比较基因组分析在三种高度保守蛋白质中鉴定出三个保守的插入缺失（DNA促旋酶A中的一个4个氨基酸的插入、ATP合酶β亚基中的一个1个氨基酸的缺失以及核糖体蛋白S2中的一个1个氨基酸的插入），这些是梭菌属簇I物种所独有的，在任何其他细菌中都未发现。对破伤风梭菌E88和产气荚膜梭菌SM101基因组中各种蛋白质的blastp搜索也鉴定出10多种仅在簇I物种中发现的蛋白质。这些结果提供了证据，表明梭菌属簇I的物种不仅在系统发育上不同，而且共享许多独特的分子特征。这些新鉴定的分子标记提供了有用的工具，以便更明确地定义和界定狭义梭菌属。我们还在磷酸甘油酸脱氢酶中鉴定出一个7 - 9个氨基酸的保守插入，它仅在嗜热栖热菌、嗜热栖热厌氧菌、嗜热栖热嗜热栖热菌和嗜热栖热嗜热栖热菌的同源物中发现，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一个定义明确的进化枝，这个插入缺失为这个梭菌簇提供了一个潜在的分子标记。
