枯草芽孢杆菌对氨氮应答的转录组及sRNA分析

Transcriptome and sRNA analyses of the response of Bacillus subtilis to ammonia nitrogen

中文关键词: 枯草芽孢杆菌  氨氮应答  转录组  差异表达基因  sRNA分析

英文关键词: Bacillus subtilis  Response to ammonia nitrogen  Transcriptome  Differentially expressed genes  sRNA analysis

中文摘要:

      为探索枯草芽孢杆菌(Bacillus subtilis)脱氮的分子机制，筛选枯草芽孢杆菌对氨氮的分子生态学应答相关候选基因及small RNA(sRNA)，本研究对处于富含氨氮环境和对照组的枯草芽孢杆菌R47进行原核链特异性转录组及sRNA分析，并采用Real-time PCR方法检测差异表达基因的相对表达量。结果显示，平均每个测序样本得到约1.40×107条reads。对照组与处理组DESeq2分析得到3918个差异表达基因，并富集在KEGG数据库中的176个信号通路，其中，包括8个与适应富含氨氮环境相关的信号通路(细菌双组分系统通路、精氨酸生物合成、嘌呤代谢等)，同时发现，epsA、tasA、sinR、glnR、glnA、tnrA和ureABC基因可能参与枯草芽孢杆菌对氨氮的应答过程。经sRNA分析获得已注释的枯草芽孢杆菌sRNA 62条。对sRNA靶基因的分析结果显示，其有3960个对应的潜在靶基因，主要参与碳水化合物运输和新陈代谢、氨基酸转运和代谢、转录过程，其中，sRNA2073和sRNA2182对应的靶基因分别为sinR和tnrA。Real-time PCR结果显示，argH、codY、argG、glnA和glnR基因的相对表达量变化与转录组测序结果一致。本研究为进一步探究枯草芽孢杆菌污水脱氮的分子机理提供参考数据。

英文摘要:

      To explore the molecular mechanism of denitrification by Bacillus subtilis and screen out candidate genes and small RNA (sRNA) related to the response of B. subtilis to ammonia nitrogen. Transcriptome sequencing and sRNA analysis were performed on B. subtilis in both an ammonia-rich environment and a control group. The relative expression changes in differentially expressed genes were analyzed using real-time PCR. The results showed that each sequencing sample yielded approximately 1.40 × 107 reads on average. There were 3918 differentially expressed genes in the control and treatment groups as per DESeq2 analysis, which enriched 176 signaling pathways in the KEGG database, including eight signaling pathways (bacterial two-component system pathway, arginine biosynthesis, purine metabolism, and so on) adapted to the ammonia-rich environment. We found that epsA, tasA, SinR, glnR, glnA, tnrA, and ureABC genes may be involved in the response of B. subtilis to ammonia nitrogen in water. Sixty-two annotated strains of B. subtilis sRNA were obtained. The prediction and analysis results of sRNA target genes revealed that there are 3960 potential target genes involved in carbohydrate transport and metabolism, amino acid transport and metabolism, and transcription processes. Among them, the target genes corresponding to sRNA2073 and sRNA2182 were sinR and tnrA, respectively. Real-time PCR analysis showed that the relative expression changes of argH, codY, argG, glnA and glnR were consistent with transcriptome sequencing. These results provide reference data for further exploring the molecular mechanism of nitrogen removal by B. subtilis in wastewater.