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基于转录组分析猪链球菌抗氧化应激相关基因表达的变化

Transcriptome-based Analysis of Changes in Antioxidant Stress-related Gene Expression in Streptococcus suis

  • 摘要: 本研究通过转录组测序技术研究猪链球菌(Streptococcus suis)经H2O2处理后的全基因组转录水平变化,探究氧胁迫下与猪链球菌应对氧化应激过程相关的代谢通路和基因。将9型猪链球菌DN13菌株培养至对数生长后期,用PBS和H2O2分别处理15 min,将处理后的DN13菌株进行转录组测序(RNA-seq),对转录本中的差异表达基因进行KEGG和GO分析,并用实时定量PCR(real-time quantitative PCR, RT-qPCR)验证RNA-seq的分析结果。RNA-seq结果显示,DN13共检测到2 005个基因,与对照组相比,实验组有749个基因差异表达,占比37.4%。GO富集结果表明,差异表达基因在分子功能、生物学过程和细胞组分这3大类中均显著富集。KEGG富集结果表明,差异表达基因主要集中在核糖体、 ABC转运体、氨基糖和核苷酸糖的代谢以及半乳糖代谢等代谢途径中。RT-qPCR结果与RNA-seq数据的一致性好,证明RNA-seq分析结果具有可靠性。这说明猪链球菌应对氧化应激是一个涉及细菌多个途径和一系列基因表达变化的复杂过程。通过分析实验组和对照组之间DN13菌株的基因表达水平,发现在本研究中与抗氧化相关的差异表达基因的表达变化均与其功能一致,且均注释到催化活性、细胞结构体和结合这3个GO条目中,这说明转录组分析的数据可在整体上准确反映参与抗氧化应激基因表达水平的变化。

     

    Abstract: In this study, we investigated the changes in genome-wide transcript levels of Streptococcus suis after H2O2 treatment by transcriptome sequencing to explore the metabolic pathways and genes associated with the process of oxidative stress response in Streptococcus suis under oxidative stress. The strain DN13 of S. suis type 9 was cultured to the late logarithmic phase and treated with PBS and H2O2 for 15 min. The transcriptome sequencing(RNA-seq) of the treated strain DN13 was performed. The differentially expressed genes in the transcripts were analyzed by KEGG and GO, and the results of RNA-seq were verified by RT-qPCR. The RNA-seq results showed that a total of 2 005 genes were detected in DN13, and 749 genes were differentially expressed in the experimental group compared to the control group, accounting for 37.4%. The GO enrichment results showed that differentially expressed genes were significantly enriched in three major categories: molecular function, biological process and cellular component. The KEGG enrichment results showed that the differentially expressed genes were mainly concentrated in the ribosome, ABC transporter, amino sugar and nucleotide sugar metabolism, and galactose metabolism metabolic pathways. The RT-qPCR results were consistent with the RNA-seq data, which proved that the RNA-seq analysis results were reliable. This suggests that the response of Streptococcus suis to oxidative stress is a complex process involving multiple bacterial pathways and a series of changes in gene expression. Analysis of gene expression levels of DN13 strains between the experimental group and control group revealed that the expression changes of differentially expressed genes associated with antioxidant in this study were all consistent with their functions and were all annotated to the three GO entries of cataly-tic activity, cellular anatomical entity and binding, suggesting that the data from transcriptome analysis can accurately reflect the changes in expression levels of genes involved in resistance to oxidative stress as a whole.

     

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