Transcriptomic analysis of Pseudomonas aeruginosa DN1 upon degradation of fluoranthene

Abstract:

[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.