Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.
Environ Sci Process Impacts. 2020 Mar 1;22(3):663-678. doi: 10.1039/c9em00605b. Epub 2020 Mar 11.
Organohalide respiring bacteria (OHRB) express reductive dehalogenases for energy conservation and growth. Some of these enzymes catalyze the reductive dehalogenation of chlorinated and brominated pollutants in anaerobic subsurface environments, providing a valuable ecosystem service. Dehalococcoides mccartyi strains have been most extensively studied owing to their ability to dechlorinate all chlorinated ethenes - most notably carcinogenic vinyl chloride - to ethene. The genomes of OHRB, particularly obligate OHRB, often harbour multiple putative reductive dehalogenase genes (rdhA), most of which have yet to be characterized. We recently sequenced and closed the genomes of eight new strains, increasing the number of available D. mccartyi genomes in NCBI from 16 to 24. From all available OHRB genomes, we classified predicted translations of reductive dehalogenase genes using a previously established 90% amino acid pairwise identity cut-off to identify Ortholog Groups (OGs). Interestingly, the majority of D. mccartyi dehalogenase gene sequences, once classified into OGs, exhibited a remarkable degree of synteny (gene order) in all genomes sequenced to date. This organization was not apparent without the classification. A high degree of synteny indicates that differences arose from rdhA gene loss rather than recombination. Phylogenetic analysis suggests that most rdhA genes have a long evolutionary history in the Dehalococcoidia with origin prior to speciation of Dehalococcoides and Dehalogenimonas. We also looked for evidence of synteny in the genomes of other species of OHRB. Unfortunately, there are too few closed Dehalogenimonas genomes to compare at this time. There is some partial evidence for synteny in the Dehalobacter restrictus genomes, but here too more closed genomes are needed for confirmation. Interestingly, we found that the rdhA genes that encode enzymes that catalyze dehalogenation of industrial pollutants are the only rdhA genes with strong evidence of recent lateral transfer - at least in the genomes examined herein. Given the utility of the RdhA sequence classification to comparative analyses, we are building a public web server () for the community to use, which allows users to add and classify new sequences, and download the entire curated database of reductive dehalogenases.
有机卤代呼吸菌 (OHRB) 表达还原脱卤酶以进行能量保存和生长。这些酶中的一些催化在厌氧地下环境中氯化和溴化污染物的还原脱卤，提供了有价值的生态系统服务。由于其能够将所有氯代乙稀——最显著的致癌氯乙烯——还原为乙稀，因此 Dehalococcoides mccartyi 菌株得到了最广泛的研究。OHRB 的基因组，特别是必需 OHRB 的基因组，通常含有多个假定的还原脱卤酶基因 (rdhA)，其中大多数尚未得到表征。我们最近对 8 个新菌株进行了测序和基因组封闭，使 NCBI 中可用的 D. mccartyi 基因组数量从 16 个增加到 24 个。从所有可用的 OHRB 基因组中，我们使用先前建立的 90%氨基酸两两同一性截止值对还原脱卤酶基因的预测翻译进行分类，以鉴定直系同源物组 (OGs)。有趣的是，一旦将 D. mccartyi 脱卤酶基因序列分类为 OG，在迄今为止测序的所有基因组中，大多数基因的排列都表现出惊人的同线性（基因顺序）。如果没有分类，这种组织就不会明显。高度同线性表明差异是由 rdhA 基因缺失而不是重组引起的。系统发育分析表明，大多数 rdhA 基因在 Dehalococcoidia 中有很长的进化历史，起源于 Dehalococcoides 和 Dehalogenimonas 的物种形成之前。我们还在其他 OHRB 物种的基因组中寻找同线性的证据。不幸的是，此时比较 Dehalogenimonas 的封闭基因组数量还太少。在 Dehalobacter restrictus 基因组中存在一些部分同线性的证据，但这里也需要更多的封闭基因组来确认。有趣的是，我们发现催化工业污染物脱卤的酶的 rdhA 基因是唯一具有近期水平转移强证据的 rdhA 基因——至少在本文检查的基因组中是这样。鉴于 RdhA 序列分类在比较分析中的实用性，我们正在为社区构建一个公共网络服务器（），供社区使用，允许用户添加和分类新序列，并下载还原脱卤酶的整个经校对的数据库。
