二氯喹啉酸是一种广泛应用的稻田除草剂，由于对后茬作物易产生药害，已成为制约我国南方稻田轮作的主要因素之一。微生物降解是降低二氯喹啉酸药害的有效途径。Bacillus megaterium Q3是课题组分离得到的一株二氯喹啉酸高效降解内生细菌。前期，我们对Q3的生物学及降解特征进行了系统研究，已完成全基因组序列测定和注释，但其降解的分子机制尚不清楚。本项目拟运用系统生物学方法阐明Q3降解二氯喹啉酸的调控机制和分子机理。通过对Q3在二氯喹啉酸胁迫下的基因表达进行系列RNA-seq测序，比较不同胁迫条件下的基因表达差异，从而发掘Q3的二氯喹啉酸降解酶。同时，用基因表达数据构建基因共表达网络和转录调控网络，阐明Q3降解二氯喹啉酸的调控机制，并应用分子生物学方法验证降解酶和调控因子。本课题对于理解微生物降解二氯喹啉酸的分子机理具有重要的意义，也为进一步改造和利用Q3提供理论依据和技术基础。

Quinclorac (3,7-dichloro-8-quinoline-carboxylic) is an highly selective, widely used herbicide for controlling barnyard grass and certain dicot grasses in rice. However, the quinclorac residues are phytotoxic to many crops/vegetables, which become one of the major factors that affect rice and economic crop/vegetable ration in southern china. Degrading quinclorac using microbial is an effective way to reduce its phytotoxicity. In our preliminary study, we had isolated, identified and characterized an endophytic quinclorac degrading bacterium, Bacillus megaterium Q3. We assembled the whole genome of Q3 using de novo sequencing and predicted its gene annotations. However, the molecular mechanism of quinclorac degradation in Q3 is still unclear. In this project, we will apply systems biology methods to elucidate the enzymes for quinclorac degradation and transcription factors that control the quinclorac degradation. We will use RNA-seq to monitor the gene expressions of Q3 under quinclorac stress. We will identify the enzymes for quinclorac degradation by detecting differentially expressed genes. Furthermore, we will construct gene co-expression network to identify function modules and transcription factors that relate to quinclorac degradation. We will conduct biochemistry and genetic experiments to validate the functionality of enzymes and transcription factors. The findings of this proposal will significantly advance fundamental understanding of the molecular mechanism of quinclorac degradation in Q3. It will facilitate the modification and utilization of Q3 as a quinclorac degradation bacterium in the future.