Department of Civil and Environmental Engineering, University of California, Berkeley, USA.
ISME J. 2011 Jun;5(6):1014-24. doi: 10.1038/ismej.2010.202. Epub 2011 Jan 13.
Comparative genomics of Dehalococcoides strains and an enrichment were performed using a microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus. The microarray was designed with 4305 probe sets to target 98.6% of the open-reading frames from strains 195, CBDB1, BAV1 and VS. The microarrays were validated and applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2, and their enrichment source (ANAS) to understand the genome-physiology relationships. Strains ANAS1 and ANAS2 can both couple the reduction of trichloroethene, cis-dichloroethene (DCE) and 1,1-DCE, but not tetrachloroethene and trans-DCE with growth, whereas only strain ANAS2 couples vinyl chloride reduction to growth. Comparative genomic analysis showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements or high-plasticity regions. Combined results of the two isolates closely matched the results obtained using genomic DNA of the ANAS enrichment. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny seems to be related to the presence of distinct reductive dehalogenase-encoding genes with assigned chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Overall, the microarrays are a valuable high-throughput tool for comparative genomics of unsequenced Dehalococcoides-containing samples to provide insights into their gene content and dechlorination functions.
采用针对所有可获得的脱氯菌属基因组测序的基因设计的微阵列，对 Dehalococcoides 菌株和富集物进行了比较基因组学研究。该微阵列设计了 4305 个探针组，以靶向菌株 195、CBDB1、BAV1 和 VS 的开放阅读框的 98.6%。微阵列经过验证并应用于查询最近分离的 Dehalococcoides 菌株 ANAS1 和 ANAS2 及其富集源（ANAS）的基因组，以了解基因组-生理学关系。菌株 ANAS1 和 ANAS2 都可以将三氯乙烯、顺式-二氯乙烯（DCE）和 1,1-DCE 的还原与生长偶联，但不能将四氯乙烯和反式-DCE 与生长偶联，而只有菌株 ANAS2 将氯乙烯还原与生长偶联。比较基因组分析表明，这两个菌株的基因组彼此相似，与菌株 195 相似，除了先前定义的整合元件或高可塑性区域内的基因。两个分离株的综合结果与使用 ANAS 富集物的基因组 DNA 获得的结果非常吻合。基因组相似性，以及菌株 ANAS1、ANAS2 和 195 对氯化乙烯的不同使用，表明密切相关的菌株在生理上可能不同。这种生理学与核心基因组系统发育之间的不匹配似乎与存在不同的还原脱卤酶编码基因有关，这些基因具有特定的氯化乙烯功能（pceA、tceA 在菌株 195 中；tceA 在菌株 ANAS1 中；vcrA 在菌株 ANAS2 中）。总体而言，微阵列是一种用于未测序的含 Dehalococcoides 样品比较基因组学的有价值的高通量工具，可以深入了解其基因组成和脱氯功能。
