Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China.
Arch Microbiol. 2019 Sep;201(7):907-918. doi: 10.1007/s00203-019-01660-w. Epub 2019 Apr 17.
The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CH-degrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization.
在过去的十年中，由于氯乙酰胺类除草剂（CH）具有致癌性，其在环境中的归宿引起了越来越多的关注。尽管微生物在 CH 降解中发挥了重要作用，但地杆菌属（Sphingomonas） DC-6 是第一个被报道的 CH 矿化细菌。本研究对菌株 DC-6 的全基因组进行了测序，并利用菌株 DC-6 与其他 3 株部分 CH 降解细菌（鞘氨醇单胞菌（Sphingobium） quisquiliarum DC-2、地杆菌（Sphingobacterium） baderi DE-13 和鞘氨醇单胞菌（Sphingobium） sp. MEA3-1）进行了比较基因组分析。16S rDNA 系统发育分析表明，菌株 DC-2、MEA3-1 和 DE-13 亲缘关系密切，而菌株 DC-6 与其他 3 株菌的遗传关系相对较远。鉴定出的负责上下游途径的 CH 降解基因，包括 cndA、cmeH、MEAXY 和 meaAB，均位于移动元件蛋白附近的保守 DNA 片段（或遗传岛）中。NCBI 数据库中的蛋白 BLAST 显示，cndA 和 cmeH 存在于从各种生境中分离的其他测序菌株的基因组中；然而，这些宿主菌株的基因组成与其他鞘氨醇单胞菌完全不同，上游途径基因的密码子使用也与下游途径不同。这些结果表明，菌株 DC-6 中 CH 降解的上下游途径是通过水平基因转移和基因组合进化而来的。此外，环裂解途径的基因不保守，可能是由细菌直接降解羟基喹啉而产生的。本研究为 CH 矿化的进化策略和微生物代谢途径提供了新的见解。
