不同遗传背景下QsvR调控副溶血弧菌基因表达的转录组分析

Transcriptome analysis of QsvR regulating gene expression of Vibrio parahaemolyticus with different genetic backgrounds

摘要:

【背景】OpaR是副溶血弧菌群体感应系统的核心调控因子；QsvR是AraC家族转录调控因子，与OpaR之间具有相互调控作用；此外，QsvR对基因表达的调控作用受OpaR的影响，但是影响程度并未完全阐明。【目的】探究在野生株(wild-type, WT)和opaR基因突变株(ΔopaR)的遗传背景下QsvR的转录调控元，分析OpaR对QsvR基因表达调控的影响。【方法】分别以WT和ΔopaR为参照，采用Illumina HiSeq测序平台进行比较转录组学研究，分析生物膜形成条件下qsvR基因突变株(ΔqsvR)和ΔqsvRΔopaR的基因表达情况。【结果】在WT遗传背景下，QsvR共调控1 735个基因的转录(调控元1)，其中被激活的基因有855个，被抑制的基因有880个；在ΔopaR遗传背景下，QsvR共调控1 187个基因的转录(调控元2)，其中被激活的基因有533个，被抑制的基因有654个。调控元1和调控元2之间共有517个重叠基因，且QsvR对绝大多数重叠基因的调控关系相反。基因属性分类(gene ontology, GO)数据库富集分析结果显示，调控元1和调控元2中分别有467个和204个基因注释到分子功能、细胞组分和生物学过程3个一级分类和30个二级分类；京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)对代谢途径的分析结果显示，调控元1和调控元2中分别有372和678个基因归到30个代谢通路中(Q value＜0.05)，调控元1中的基因主要集中在代谢、基因信息处理和环境信息处理上，而调控元2中的基因主要集中在细胞代谢通路上。蛋白相邻类的聚簇(cluster of orthologous groups of proteins, COG)数据库分类结果显示，调控元1和调控元2中的基因主要涉及氨基酸转运与代谢、信号转导、能量产生与转换、一般功能预测基因和未知功能基因等。此外，调控元1和调控元2中还含有大量调控因子基因和推定的c-di-GMP代谢基因，以及若干极生鞭毛基因、荚膜多糖基因、胞外多糖合成基因、IV型菌毛合成基因、III型分泌系统基因和VI型分泌系统基因等。【结论】QsvR是副溶血弧菌中的全局性调控因子，控制着大量基因的转录。QsvR对靶基因的调控关系及QsvR调控元组成均受OpaR的影响。

Abstract:

[Background] OpaR is the master quorum sensing regulator of Vibrio parahaemolyticus. QsvR, an AraC-type transcriptional regulator, has reciprocal regulatory activities with OpaR. The regulatory effect of QsvR on gene expression is affected by OpaR, while their relationship in gene regulation remains to be fully elucidated. [Objective] To investigate QsvR regulons in the wild type (WT) and the opaR mutant (ΔopaR), and thus determine the effect of OpaR on the gene regulation of QsvR in V. parahaemolyticus. [Methods] Illumina HiSeq was employed to mine the differentially expressed genes in the qsvR mutant (ΔqsvR) or ΔqsvRΔopaR relative to that in WT or ΔopaR under the biofilm formation growth condition. [Results] QsvR regulated 1 735 genes (regulon 1) in the WT background, including 855 genes activated and 880 genes repressed. QsvR regulated 1 187 genes (regulon 2) in the ΔopaR background, including 533 genes activated and 654 genes repressed. There were 517 common genes shared by regulons 1 and regulons 2, and most of these genes were oppositely regulated by QsvR between the two regulons. According to the results of gene ontology (GO) annotation, 467 and 204 genes from regulons 1 and regulons 2 were respectively annotated to three categories (biological process, molecular function, and cellular component) and thirty sub-categories. The results of Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment showed that 372 and 678 genes from regulons 1 and regulons 2 were respectively enriched in 30 signaling pathways (Q value＜0.05). The genes in regulon 1 were mainly enriched in cellular metabolism, genetic information processing, and environmental information processing, and those in regulon 2 in cellular metabolism. The classification results obtained with the cluster of orthologous groups of proteins (COG) showed that the genes in regulons 1 and regulons 2 were mainly involved in amino acid transport and metabolism, signal transduction mechanisms, energy production and conversion, general function prediction only, and function unknown. In addition, the regulons 1 and regulons 2 contained a large number of regulatory genes and putative c-di-GMP metabolism-associated genes, as well as some polar flagellar genes, capsular polysaccharide genes, exopolysaccharide synthesis genes, type IV pili-associated genes, type III secretion system genes, and type VI secretion system genes. [Conclusion] QsvR was a global regulator in V. parahaemolyticus, controlling the transcription of a large number of genes. OpaR affected the regulatory actions of QsvR on its target genes and the composition of QsvR regulon.