Qu Yuanyuan, Ma Qiao, Liu Ziyan, Wang Weiwei, Tang Hongzhi, Zhou Jiti, Xu Ping
State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China.
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
Mol Microbiol. 2017 Dec;106(6):905-918. doi: 10.1111/mmi.13852. Epub 2017 Oct 23.
Indole, an important signaling molecule as well as a typical N-heterocyclic aromatic pollutant, is widespread in nature. However, the biotransformation mechanisms of indole are still poorly studied. Here, we sought to unlock the genetic determinants of indole biotransformation in strain Cupriavidus sp. SHE based on genomics, proteomics and functional studies. A total of 177 proteins were notably altered (118 up- and 59 downregulated) in cells grown in indole mineral salt medium when compared with that in sodium citrate medium. RT-qPCR and gene knockout assays demonstrated that an indole oxygenase gene cluster was responsible for the indole upstream metabolism. A functional indole oxygenase, termed IndA, was identified in the cluster, and its catalytic efficiency was higher than those of previously reported indole oxidation enzymes. Furthermore, the indole downstream metabolism was found to proceed via the atypical CoA-thioester pathway rather than conventional gentisate and salicylate pathways. This unusual pathway was catalyzed by a conserved 2-aminobenzoyl-CoA gene cluster, among which the 2-aminobenzoyl-CoA ligase initiated anthranilate transformation. This study unveils the genetic determinants of indole biotransformation and will provide new insights into our understanding of indole biodegradation in natural environments and its functional studies.
吲哚作为一种重要的信号分子以及典型的含氮杂环芳香污染物，在自然界中广泛存在。然而，吲哚的生物转化机制仍鲜有研究。在此，我们试图基于基因组学、蛋白质组学和功能研究揭示菌株贪铜菌属SHE中吲哚生物转化的遗传决定因素。与柠檬酸钠培养基中的细胞相比，在吲哚矿物盐培养基中生长的细胞中共有177种蛋白质发生显著变化（118种上调和59种下调）。RT-qPCR和基因敲除试验表明，一个吲哚加氧酶基因簇负责吲哚的上游代谢。在该基因簇中鉴定出一种功能性吲哚加氧酶，命名为IndA，其催化效率高于先前报道的吲哚氧化酶。此外，发现吲哚的下游代谢通过非典型的辅酶A硫酯途径而非传统的龙胆酸盐和水杨酸盐途径进行。这一不同寻常的途径由一个保守的2-氨基苯甲酰辅酶A基因簇催化，其中2-氨基苯甲酰辅酶A连接酶启动邻氨基苯甲酸的转化。本研究揭示了吲哚生物转化的遗传决定因素，并将为我们理解自然环境中吲哚的生物降解及其功能研究提供新的见解。
