sRNA伴侣蛋白Hfq敲除条件下沙门菌的转录组分析

Transcriptome analysis of sRNA chaperone Hfq deletion mutant in Samonella

为探明沙门菌(Salmonella)在sRNA伴侣蛋白Hfq敲除条件下转录组变化情况。本试验采用HiSeq测序平台对沙门菌LT2菌株及其Hfq敲除株进行高通量测序,通过DESeq2差异分析方法筛选敲除sRNA伴侣蛋白Hfq条件下的差异表达基因,对其进行生物信息学GO功能显著性富集分析和Pathway显著性富集分析。结果显示,对照组和试验组分别得到12 753 534条、8 254 308条Clean Reads。通过DESeq2差异分析获得差异基因1 055个,其中表达上调基因516个,表达下调基因539个。GO功能显著性富集分析表明显著差异表达基因主要富集在钴胺素代谢过程、钴胺素生物合成过程、碳水化合物代谢过程等生物过程中。Pathway显著性富集分析表明显著差异表达基因富集到细菌趋化性、丙酸代谢和碳代谢等11个信号通路中。结果表明,本试验应用RNA-seq技术丰富了sRNA伴侣蛋白Hfq调控基因数量,筛选出20个受伴侣蛋白Hfq调控的显著差异表达基因,其中4个基因功能及编码蛋白未知,注释了差异表达基因的生物学功能及信号通路,推断Hfq在细菌对数期主要通过影响营养提供和趋化性等途径,继而影响细菌的正常生理活动,为Hfq协同sRNA的调控机理研究及sRNA靶基因的筛选奠定了基础。

To study the transcriptome changes of sRNA chaperone Hfq deletion mutant in Samonella.In this study,high-throughput sequencing of Salmonella LT2 strain and its Hfq deletion mutant was carried out by using HiSeq sequencing platform.The differentially expressed genes of chaperone Hfq deletion mutant were screened by DESeq2 differential analysis method,and the differentially expressed genes were analyzed by bioinformatics GO function significant enrichment analysis and pathway significant enrichment analysis.There were 12753534 and 8254308 Clean Reads in the control group and the experimental group respectively.1055 differential genes were obtained by DESeq2 differential analysis,of which 516 genes were up-regulated and 539 genes were down-regulated.Significant enrichment analysis of GO function indicated that significant differentially expressed genes were mainly involved in the cobalamin metabolic process,cobalamin biosynthetic process and carbohydrate metabolic process.Pathway significant enrichment analysis showed that significantly differentially expressed genes were enriched in 11 signaling pathways,including bacterial chemotaxis,propanoate metabolism and carbon metabolism.This study enriched the number of Hfq regulatory genes by using RNA-seq technology,screened 20 significantly differentially expressed genes were regulated by chaperone Hfq,Among them,4 genes had unknown function and encoded protein.After annotating the biological functions and signaling pathways of genes,it is concluded that Hfq influences the normal physiological activities of bacteria mainly through influencing nutrient supply and chemotaxis in the logarithmic phase of bacteria,which laid the foundation for the regulation of Hfq-sRNA and the screening of sRNA target genes.