基于转录组分析铜绿假单胞菌DN1降解荧蒽特性

Transcriptomic analysis of Pseudomonas aeruginosa DN1 upon degradation of fluoranthene

[背景]铜绿假单胞菌DN1是一株从石油污染土壤中分离筛选到的具有广谱降解功能的菌株。[目的]深入了解荧蒽胁迫条件下铜绿假单胞菌DN1降解污染物过程中重要的降解相关基因信息。[方法]通过高通量测序技术对铜绿假单胞菌DN1进行转录组测序,对其所有的转录本进行KEGG (kyoto encyclopedia of genes and genomes)分类和Pathway注释、GO (gene ontology)分类和富集分析。[结果]转录组测序显示:与对照组相比,荧蒽诱导组检测到6 189个基因,其中1 919个基因上调表达,1 603个基因下调表达。KEGG注释分析显示差异上调表达基因匹配到了112个KEGG代谢途径,注释到"代谢途径"的1 408个基因(约占总差异基因的73.4%)中有317个基因参与了碳氢化合物代谢及含有苯环结构的异源生物质的生物降解,占"代谢途径"的16.53%,暗示了菌株DN1降解荧蒽可能与这些途径有密切关系。另外,主要代谢途径中的差异表达基因主要集中在ABC转运系统、氨基酸生物合成、双组分系统及碳代谢,这些途径大多数参与了底物的识别转运、信号转导及基因表达调控。[结论]进一步拓展了铜绿假单胞菌DN1在荧蒽胁迫条件下的代谢途径和逆境反应,也为微生物修复环境污染物研究夯实了理论基础。

[Background] Pseudomonas aeruginosa DN1, isolated from a petroleum-contaminated soil, exhibits a versatile metabolism and can utilize both n-alkanes and aromatic hydrocarbons. [Objective] The aim of this study was to fully understand the expression of vital genes for fluoranthene degradation and the changes of transcriptional spectrum of the DN1 in response to fluoranthene. [Methods] An RNA-Seq-based transcriptome was conducted for a global analysis of the DN1 in media with fluoranthene and glucose respectively, and all transcripts were subjected to KEGG classification and pathway annotation, GO classification and enrichment analysis. [Results] A total of 6 189 assembled contigs were obtained and analyzed in detail. In contrast to control group with glucose, 1 919 genes that corresponded to this degradation in the DN1 were found to be up-regulated and 1 603 genes were found to be down-regulated. KEGG pathway analysis showed that 112 KEGG pathways with up-regulated expression were variant, and 317 of the 1 408 genes that were about 73.4% of total differential genes annotated to the "metabolism" pathway involved in carbohydrate metabolism and xenobiotics biodegradation and metabolism, accounting for 16.53% of the "metabolism" pathway, which suggested that fluoranthene degradation by the DN1 may be closely related to these pathways. Moreover, the differentially expressed genes of primary metabolic pathways were identified and the results indicated that the main pathways, such as ABC transporters, biosynthesis of amino acids, two-component system and carbon metabolism, involved mostly in substrates recognition and transport, signal transduction and gene expression regulation. [Conclusion] The results will be expected to enhance our understanding on fluoranthene metabolic pathway and stress response of the DN1 in future studies, as well as lay a solid theoretical foundation for the research on microbial remediation of environmental pollutants.