sRNA SdsR敲除后沙门菌的转录组分析

Transcriptome Analysis of Salmonella After sRNA SdsR Knockout

sRNA SdsR是σS调节子的成员,控制着细菌全局适应性反应,为探明sRNA SdsR敲除后沙门菌的转录组变化情况,本研究利用Illumina NovaSeq 6000高通量测序技术,对沙门菌LT2标准株和sRNA SdsR缺失株进行高通量测序,全方位预测SdsR的潜在靶基因的种类和功能;采用DESeq对基因表达进行差异分析,并对差异表达基因进行GO富集分析和KEGG pathway分析,进一步筛选差异表达基因行使的生物学功能以及所参与的信号途径;通过qRT-PCR验证部分差异基因结果的准确性。结果显示:对照组和实验组共筛选出25 731 760条和26 866 200条Clean Reads,DESeq差异分析获得差异基因共127个,其中基因表达量下调74个,上调53个;GO富集分析显示,显著差异表达基因主要富集在二醇分解代谢过程、乙二醇分解代谢过程等684个生物过程;KEGG pathway分析显示,显著差异表达基因主要参与丙酸代谢、双组分系统、丙氨酸、天冬氨酸和谷氨酸代谢等27个信号途径;对筛选的10个差异基因进行qRT-PCR进行验证,结果显示,差异表达基因的mRNA转录水平与DESeq预测的结果上下调节趋势完全符合,表明测序结果可靠。本研究丰富了sRNA SdsR的靶基因数目,为进一步研究sRNA SdsR的作用机理、调控机制以及沙门菌的致病机制提供了基础。

sRNA SdsR is a member of the σSregulator, which controls the global adaptive response of bacteria. To investigate the transcriptome changes of Salmonella after sRNA SdsR knockout, the Illumina NovaSeq 6000 high-throughput sequencing technology was used to perform high-throughput sequencing of Salmonella LT2 standard strains and sRNA SdsR deletion strains, and comprehensively predict the types and functions of potential target genes of SdsR. DESeq was used for differential analysis of gene expression, GO enrichment and KEGG pathway analyses of differentially expressed genes were used to further screen the biological functions of differentially expressed genes and signal pathways involved. The accuracy of the results of some differential genes was verifi ed by qRTPCR. The results showed that 25,731,760 and 26,866,200 Clean Reads were screened in the control group and experimental group.DESeq differential analysis obtained a total of 127 differential genes, of which 74 were down-regulated and 53 were up-regulated. GO enrichment analysis showed that the signifi cantly differentially expressed genes were mainly enriched in 684 biological processes such as glycol catabolism and ethylene glycol catabolism. KEGG pathway analysis revealed that the significantly differentially expressed genes were mainly involved in 27 signal pathways such as propionic acid metabolism, two-component system, alanine, aspartic acid and glutamic acid metabolism. The 10 differential genes screened were verifi ed by qRT-PCR. The results showed that the mRNA transcription levels of differentially expressed genes were in full compliance with the upward and downward adjustment trends as predicted by DESeq,indicating that the sequencing results were reliable. This study enriched the number of target genes of sRNA SdsR and provided a basis for further research on the mechanisms of action, regulation and pathogenicity of sRNA SdsR.