A Recently Assembled Degradation Pathway for 2,3-Dichloronitrobenzene in Diaphorobacter sp. Strain JS3051.
A Recently Assembled Degradation Pathway for 2,3-Dichloronitrobenzene in Diaphorobacter sp. Strain JS3051.
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最近组装的 2,3-二氯硝基苯在 Diaphorobacter sp. 中的降解途径。
DOI：
10.1128/mbio.02231-21
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发表时间：
2021-08-31
期刊：
影响因子：
6.4
通讯作者：
Zhou NY
中科院分区：
文献类型：
--
作者：
Li T;Gao YZ;Xu J;Zhang ST;Guo Y;Spain JC;Zhou NY
由于人类产生的硝基芳香族化合物进入生物圈的时间相对较晚，因此探索这些新近进化的分解代谢途径可以为细菌的适应性进化机制提供线索。硝基芳烃双加氧酶与萘双加氧酶具有共同祖先的概念已得到证实。Diaphorobacter sp.菌株JS3051利用有毒的人为化合物2,3-二氯硝基苯（23DCNB）作为唯一的碳、氮和能量来源进行生长，但其代谢途径及其来源尚不清楚。在这里，我们建立了一个基因簇（dcb），编码一个nag样双加氧酶，负责23DCNB分子的初始氧化。2,3-二氯硝基苯双加氧酶体系（DcbAaAbAcAd）催化23DCNB转化为3,4-二氯邻苯二酚（34DCC）。位点定向诱变研究表明，DcbAc的残基204对23DCNB双加氧酶的底物特异性至关重要。谷氨酸在23DCNB双加氧酶204位的存在是nag样双加氧酶中独特的。遗传、生化和结构证据表明，23DCNB双加氧酶与Acidovorax sp.菌株JS42的2-硝基甲苯双加氧酶的亲缘关系比与Diaphorobacter sp.菌株JS3050的34DCNB双加氧酶的亲缘关系更密切，后者与菌株JS3051分离自同一位点。编码34DCC分解代谢酶的基因簇（dcc）也位于距离dcb基因2.5 Mb的染色体上，与knackmussii假单胞菌B13菌株的clc操纵子同源。异源表达的DccA催化34DCC具有高亲和力和催化效率。这项工作不仅建立了23DCNB矿化的分子机制，而且增强了对硝基arenes分解代谢途径最新演变的认识。由于人为的硝基芳香族化合物进入生物圈的时间相对较晚，探索最近进化的分解代谢途径可以为细菌的适应性进化机制提供线索。硝基芳烃双加氧酶与萘双加氧酶具有共同祖先的概念已得到证实。但它们的系统发育以及它们是如何对新型硝基芳香族化合物做出反应而进化的，在很大程度上是未知的。对23DCNB降解分子基础的研究表明，同一位点不同分离株的两种DCNB异构体的分解代谢途径来源于不同的近代起源。整合催化亚基的结构模型和酶活性数据提供了关于如何根据新底物的结构选择最近修饰的酶的新见解。本研究提高了对细菌对新化学物质反应的分解代谢途径适应性进化的认识和预测。
Because anthropogenic nitroaromatic compounds have entered the biosphere relatively recently, exploration of the recently evolved catabolic pathways can provide clues for adaptive evolutionary mechanisms in bacteria. The concept that nitroarene dioxygenases shared a common ancestor with naphthalene dioxygenase is well established. ABSTRACT Diaphorobacter sp. strain JS3051 utilizes 2,3-dichloronitrobenzene (23DCNB), a toxic anthropogenic compound, as the sole carbon, nitrogen, and energy source for growth, but the metabolic pathway and its origins are unknown. Here, we establish that a gene cluster (dcb), encoding a Nag-like dioxygenase, is responsible for the initial oxidation of the 23DCNB molecule. The 2,3-dichloronitrobenzene dioxygenase system (DcbAaAbAcAd) catalyzes conversion of 23DCNB to 3,4-dichlorocatechol (34DCC). Site-directed mutagenesis studies indicated that residue 204 of DcbAc is crucial for the substrate specificity of 23DCNB dioxygenase. The presence of glutamic acid at position 204 of 23DCNB dioxygenase is unique among Nag-like dioxygenases. Genetic, biochemical, and structural evidence indicate that the 23DCNB dioxygenase is more closely related to 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 than to the 34DCNB dioxygenase from Diaphorobacter sp. strain JS3050, which was isolated from the same site as strain JS3051. A gene cluster (dcc) encoding the enzymes for 34DCC catabolism, homologous to a clc operon in Pseudomonas knackmussii strain B13, is also on the chromosome at a distance of 2.5 Mb from the dcb genes. Heterologously expressed DccA catalyzed ring cleavage of 34DCC with high affinity and catalytic efficiency. This work not only establishes the molecular mechanism for 23DCNB mineralization, but also enhances the understanding of the recent evolution of the catabolic pathways for nitroarenes. IMPORTANCE Because anthropogenic nitroaromatic compounds have entered the biosphere relatively recently, exploration of the recently evolved catabolic pathways can provide clues for adaptive evolutionary mechanisms in bacteria. The concept that nitroarene dioxygenases shared a common ancestor with naphthalene dioxygenase is well established. But their phylogeny and how they evolved in response to novel nitroaromatic compounds are largely unknown. Elucidation of the molecular basis for 23DCNB degradation revealed that the catabolic pathways of two DCNB isomers in different isolates from the same site were derived from different recent origins. Integrating structural models of catalytic subunits and enzymatic activities data provided new insight about how recently modified enzymes were selected depending on the structure of new substrates. This study enhances understanding and prediction of adaptive evolution of catabolic pathways in bacteria in response to new chemicals.