Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):2176-2181. doi: 10.1099/ijs.0.057919-0. Epub 2014 Mar 27.
The bacteria belonging to the class Dehalococcoidia, due to their ability to dehalogenate chlorinated compounds, are of much interest for bioremediation of contaminated sites. We report here comparative analyses on different genes/proteins from the genomes of members of the class Dehalococcoidia. These studies have identified numerous novel molecular markers in the forms of conserved signature indels (CSIs) in broadly distributed proteins and conserved signature genes/proteins (CSPs), which are uniquely found in members of the class Dehalococcoidia, but except for an isolated exception, they are not found in other sequenced bacterial genomes. Of these molecular markers, nine CSIs in divergent proteins and 19 CSPs are specific for members of the genera Dehalococcoides and Dehalogenimonas, providing potential molecular markers for the bacterial class Dehalococcoidia. Additionally, four CSIs in divergent proteins and 28 CSPs are only found in all members of the genus Dehalococcoides for which genome sequences are available, but they are absent in Dehalogenimonas lykanthroporepellens and in other bacteria. The gene sequences of several of these CSPs exhibiting specificity for the genus Dehalococcoides or the class Dehalococcoidia are highly conserved and PCR primers based upon them provide a novel means for identification of other related bacteria. Two other CSIs identified in this study in the SecD and aspartate carbomyltransferase proteins weakly support an affiliation of the class Dehalococcoidia with the other members of the phylum Chloroflexi.
属于脱卤球菌目（Dehalococcoidia）的细菌由于其脱卤化的能力，对于污染场地的生物修复具有重要意义。我们在此报告了对脱卤球菌目成员的不同基因/蛋白质的比较分析。这些研究在广泛分布的蛋白质和保守特征基因/蛋白质（CSPs）中发现了许多新的分子标记，这些分子标记以保守特征插入缺失（CSIs）的形式存在，它们在脱卤球菌目成员中独特存在，但除了一个孤立的例外，它们在其他测序的细菌基因组中不存在。在这些分子标记中，9 个在分歧蛋白质中的 CSI 和 19 个 CSP 是特定于脱卤单胞菌属（Dehalococcoides）和脱卤菌属（Dehalogenimonas）的成员，为脱卤球菌目提供了潜在的分子标记。此外，在所有可获得基因组序列的脱卤单胞菌属成员中仅发现了 4 个在分歧蛋白质中的 CSI 和 28 个 CSP，但在脱卤菌属（Dehalogenimonas）lykanthroporepellens 和其他细菌中不存在。这些 CSP 中的几个基因序列表现出对脱卤单胞菌属或脱卤球菌目的特异性，并且它们高度保守，基于它们的 PCR 引物提供了一种鉴定其他相关细菌的新方法。在这项研究中在 SecD 和天冬氨酸转氨甲酰酶蛋白中鉴定的另外两个 CSI 微弱地支持脱卤球菌目与其他丝状绿菌门成员的关联。
