Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
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DOI：
10.1371/journal.pgen.1000714
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Spormann AM
中科院分区：
文献类型：
--
作者：
McMurdie PJ;Behrens SF;Müller JA;Göke J;Ritalahti KM;Wagner R;Goltsman E;Lapidus A;Holmes S;Löffler FE;Spormann AM
氯乙烯（VC）是一种人类致癌物和广泛的优先污染物。在这里，我们报告的第一个，据我们所知，完整的基因组序列的微生物能够呼吸VC，Dehalococcoides物种VS和BAV 1菌株。值得注意的是，各自的VC还原酶编码基因，vcrAB和bvcAB，被发现嵌入在不同的基因组岛（GEI）与不同的预测整合位点，这表明这些基因是通过不同的机制水平和独立地获得。一项包括两个先前测序的Dehalococcoides基因组的比较分析揭示了一个上下文保守的核心，该核心被Ori附近的两个高可塑性区域（HPR）打断。这些HPR包含在四种Dehalococcoides基因组中鉴定的大多数GEI和菌株特异性基因，包括插入序列（IS）在内的大量重复元件，以及96个rdhAB中的91个，rdhAB是在有机卤化物呼吸中编码末端还原酶的基因。只有三个核心rdhA orthopathy组被确定，只有一个这些组是支持的同线性。核心rdhAB的数量少，与每个基因组的高rdhAB数量（在VS菌株中高达36个），以及它们与GEI和其他水平转移特征的共定位形成对比，表明通过有机卤化物呼吸的生态位适应是Dehalococccoides的基本生态策略。这种适应是通过多种重组机制实现的，这些机制主要局限于任何自由生活的微生物中最小的一种非常稳定、同线、流线型基因组的HPR内。 Dehalococcoides是自由生活的沉积物和地下细菌，具有非常小的流线型基因组和不寻常的生态位专业化程度。这些严格厌氧的细菌完全通过一种新型的呼吸作用获得代谢能量，这种呼吸作用导致有机氯中氯化物的还原消除，其中许多是优先污染物。在这篇文章中，我们比较了第一个完整的基因组序列的Dehalococcoides菌株生长通过呼吸氯乙烯（VC），人类致癌物质和丰富的地下水污染物。我们的工作提供了新的见解Dehalococcoides染色体的组织和进化，确定在染色体中的新基因的具体位置，如负责VC生长的基因整合，并产生这些脱氯细菌如何适应人为污染的线索。这一信息揭示了新的光Dehalococcoides生物学和生态学，与加强生物修复，以保护日益减少的饮用水水库的影响。
Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism. Dehalococcoides are free-living sediment and subsurface bacteria with remarkably small, streamlined genomes and an unusual degree of niche specialization. These strictly anaerobic bacteria gain metabolic energy exclusively through a novel type of respiration that results in reductive elimination of chlorides from organochlorines, many of which are priority pollutants. In this article, we compare the first complete genome sequences of Dehalococcoides strains that grow via respiration of vinyl chloride (VC), a human carcinogen and abundant groundwater pollutant. Our work provides novel insights into Dehalococcoides chromosome organization and evolution, identifies specific positions in the chromosomes where new genes—like the genes responsible for growth on VC—are integrated, and generates clues how these dechlorinating bacteria adapt to anthropogenic contamination. This information sheds new light on Dehalococcoides biology and ecology, with implications for enhanced bioremediation to protect dwindling drinking water reservoirs.