Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
mBio. 2013 Aug 6;4(4):e00379-13. doi: 10.1128/mBio.00379-13.
The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration.
Genome sequencing has identified, for the first time, chlorate reduction composite transposons. These transposons are constructed with flanking insertion sequences that differ in type and orientation between organisms, indicating that this mobile element has formed multiple times and is important for dissemination. Apart from core metabolic enzymes, very little is known about the genetic factors involved in chlorate reduction. Comparative analysis has identified several genes that may also be important, but the relative absence of accessory genes suggests that this mobile metabolism relies on host systems for electron transport, regulation, and cofactor synthesis. Phylogenetic analysis of Cld and ClrA provides support for the hypothesis that chlorate reduction was built multiple times from type II dimethyl sulfoxide (DMSO) reductases and cld. In at least one case, cld has been coopted from a perchlorate reduction island for this purpose. This work is a significant step toward understanding the genetics and evolution of chlorate reduction.
为了深入了解代谢，我们分析了六种细菌菌株中氯酸盐还原的基因。新分离的氯酸盐还原菌（Shewanella algae ACDC）和之前分离的三种菌株（Ideonella dechloratans、Pseudomonas sp. strain PK 和 Dechloromarinus chlorophilus NSS）进行了基因组测序，并与已发表的序列（Alicycliphilus denitrificans BC 质粒 pALIDE01 和 Pseudomonas chloritidismutans AW-1）进行了比较。基因组从头组装未能连接参与氯酸盐还原的基因附近的区域，这表明存在重复区域。使用生物信息学方法和连接碎片化的连续体的完成 PCR，我们发现氯酸盐还原基因被插入序列包围，在所有四个新测序的菌株中形成复合转座子。这些插入序列划定了具有潜在横向移动能力的区域，并定义了一组可能对氯酸盐还原很重要的基因。除了核心代谢成分外，我们还通过比较分析和可视化突出了几个这样的基因。系统发育分析将氯酸盐还原酶置于功能多样的 II 型二甲基亚砜（DMSO）还原酶功能群内，该酶群是对氯酸盐具有反应性的更大酶家族的一部分。围绕亚氯酸歧化酶（cld）的区域以及其在β变形杆菌 Cld 群聚类中的系统发育聚类的核苷酸法医分析表明，cld 至少从一种高氯酸盐还原菌中转移到构建氯酸盐呼吸中一次。
基因组测序首次确定了氯酸盐还原复合转座子。这些转座子是由在生物体之间在类型和方向上都不同的侧翼插入序列构建的，这表明这种可移动元件已经多次形成，对于传播很重要。除了核心代谢酶外，人们对参与氯酸盐还原的遗传因素知之甚少。比较分析确定了几个可能也很重要的基因，但辅助基因的相对缺失表明这种可移动代谢依赖于宿主系统进行电子传递、调节和辅因子合成。Cld 和 ClrA 的系统发育分析为氯酸盐还原是从 II 型二甲基亚砜（DMSO）还原酶和 cld 多次构建的假设提供了支持。在至少一种情况下，cld 已被从高氯酸盐还原岛中选来用于此目的。这项工作是朝着理解氯酸盐还原的遗传学和进化迈出的重要一步。
