Salinero Kennan Kellaris, Keller Keith, Feil William S, Feil Helene, Trong Stephan, Di Bartolo Genevieve, Lapidus Alla
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
BMC Genomics. 2009 Aug 3;10:351. doi: 10.1186/1471-2164-10-351.
Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism.
The a priori prediction that the D. aromatica genome would contain previously characterized "central" enzymes to support anaerobic aromatic degradation of benzene proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzylsuccinate synthase (bssABC) genes (responsible for fumarate addition to toluene) and the central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex and exosortase (epsH) are also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB) gene cluster, Calvin cycle enzymes, and proteins involved in nitrogen fixation in other species (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively).
Analysis of the D. aromatica genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial species. Examples of recent gene duplication events in signaling as well as dioxygenase clusters are present, indicating selective gene family expansion as a relatively recent event in D. aromatica's evolutionary history. Gene families that constitute metabolic cycles presumed to create D. aromatica's environmental 'foot-print' indicate a high level of diversification between its predicted capabilities and those of its close relatives, A. aromaticum str EbN1 and Azoarcus BH72.
对脱氯单胞菌属芳香菌株RCB的最初兴趣源于其厌氧降解苯的能力。它还能够还原高氯酸盐并氧化氯苯甲酸、甲苯和二甲苯，这引发了人们利用这种微生物进行生物修复的兴趣。关于这种微生物的生理数据很少有报道。它被认为是一种自由生活的生物体。
先前关于芳香脱氯单胞菌基因组将包含先前已鉴定的“核心”酶以支持苯的厌氧芳香降解的预测被证明是错误的，这表明该物种中存在新的厌氧芳香降解途径。这些缺失的途径包括苄基琥珀酸合酶（bssABC）基因（负责将富马酸添加到甲苯中）和单芳烃的核心苯甲酰辅酶A途径。使用现有的TIGRfam、COG和InterPro模型进行的深入分析，以及从头创建的HMM模型，表明其生活方式高度复杂，具有大量的环境传感器和信号通路，包括相对大量的GGDEF结构域信号受体和多个群体感应传感器。许多蛋白质表明与一个尚未知晓的宿主存在相互作用，预测的细胞宿主重塑酶、效应酶、溶血素样蛋白、黏附素、一氧化氮还原酶以及III型和VI型分泌复合体的存在表明了这一点。还存在生物膜形成的证据，包括一个推测的胞外多糖复合体和外分选酶（epsH）。本文中描述的注释还揭示了一些尚未通过实验观察到的代谢途径的证据，包括一个硫氧化（soxFCDYZAXB）基因簇、卡尔文循环酶以及其他物种中参与固氮的蛋白质（分别包括核酮糖-1,5-二磷酸羧化酶/加氧酶、核糖磷酸3-表异构酶和nif基因家族）。
对芳香脱氯单胞菌基因组的分析表明，关于这种微生物物种的代谢能力和生活方式仍有许多有待了解的地方。信号传导以及双加氧酶簇中近期基因复制事件的例子存在，表明选择性基因家族扩张是芳香脱氯单胞菌进化历史中相对较新的事件。构成推测可形成芳香脱氯单胞菌环境“足迹”的代谢循环的基因家族表明，其预测能力与其近亲芳香食酸菌属菌株EbN1和偶氮弧菌BH72的预测能力之间存在高度差异。
