基于RNA-seq分析Eha调控迟缓爱德华菌抵抗酸化的作用

Deep sequencing analysis on transcriptomes of Edwardsiella tarda regulated by Eha following acidification

目的 Eha是一个影响迟缓爱德华菌(Et)胞内生存的转录调控因子,本研究有助于揭示其调控Et抵御酸的分子机制。方法用ATPase抑制剂洛霉素A1抑制巨噬细胞的酸化,菌落计数法比较酸化对野生株和eha基因缺失株胞内存活数目的影响;比较两种细菌在酸性应激实验中存活率的差异;构建pMP220-P_(eha)LacZ质粒,采用β-半乳糖苷酶实验检测eha基因的启动子在不同酸性pH值下和不同培养时间的转录活性;选择Eha转录水平最高的一个酸性pH值和培养时间,分别提取两种细菌RNA,进行RNA-Sequencing;并用qRT-PCR验证其结果。结果野生株ET13在巨噬细胞内和不同pH酸环境中的存活率明显高于缺失株,阻止酸化胞内菌数明显高于未阻止酸化的胞内菌数(P<0.05)。对数期细菌pH6.3培养基生长2h,RNA-Sequencing结果表明:eha基因缺失株转录水平和野生株相比,147个差异显著表达的基因(DEGs)(|log2Ratio|≥1),其中113个上调,34个基因下调,qRT-PCR随机抽样,和RNA-Sequencing表达趋势呈强相关。147个基因采用GO数据库进行功能聚类,分成25类,主要涉及细菌加工、定位、代谢、结合、催化、运输、细胞成份;基于KEGG通路的富集分析,有130个可以富集到55条通路中,包括与氨基酸、核苷酸、脂质代谢及铁的转运等路径,涉及基因较多的有双组分系统、ABC转运系统、不同环境中的微生物代谢和次级代谢产物等路径。结论在酸性生存环境,Eha对Et的转录组呈多途径、多基因的适应性的全局性调控。

Our studies tried to demonstrate Eha（Et haemolysin activator）could regulate the resistance of the bacterium against acidification to survive in the macrophage and explain its underlying molecular mechanism.When the bacteria infected the macrophages at time intervals,intracellular survival rate in bafilomycin-treated macrophages was higher than that with untreated cells,and the rate of wild type ET 13 was higher than that of its eha mutant,respectively（P〈0.05）.The survival rate of the wild type was higher than that of the mutant under acid treatment（P〈0.05）.To determine the conditions that induced the highest eha expression,we constructed a pMP220-P_（eha）LacZ plasmid and determined the lacZ expression under different conditions.After exposure of pH6.3 medium for 2h time,we performed the whole transcriptomic profiles of the wild type and mutant by RNA-sequencing.We identified 147 differentially-expressed genes（｜log2 ratio｜≥1）,113 and 34 of which were significantly up-and down-regulated,respectively in the mutant,comparing with the wild type.These findings were validated by qRTPCR.GO functional analysis revealed that these genes were divided into 25 categories,including the bacterial catalysis,cellular composition,combination,localization,metabolism,processing,and transportation.Based on the KEGG database,these genes were distributed in 55 pathways,such as two-component system,ABC transporters,and microbial metabolism in diverse environments.Overall,Eha is an important regulator to affect all kinds of target genes and pathways for E.tardato adapt to an acid environment.These results could be helpful for further investigations of the mechanisms by which E.tardasurvives in macrophages.