Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India.
Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India.
Gene. 2020 Sep 10;755:144909. doi: 10.1016/j.gene.2020.144909. Epub 2020 Jun 19.
In the microbial world, bacteria are the most effective agents in petroleum hydrocarbons (PHs) degradation, utilization/mineralization and they serve as essential degraders of crude oil contaminated environment. Some genes and traits are involved in the hydrocarbon utilization process for which transcriptome analyses are important to identify differentially expressed genes (DEGs) among different conditions, leading to a new understanding of genes or pathways associated with crude oil degradation. In this work, three crude oil utilizing Pseudomonas aeruginosa strains designated as N002, TP16 and J001 subjected to transcriptome analyses revealed a total of 81, 269 and 137 significant DEGs. Among them are 80 up-regulated genes and one downregulated gene of N002, 121 up- regulated and 148 down-regulated genes of TP16, 97 up-regulated and 40 down-regulated genes of J001 which are involved in various metabolic pathways. TP16 strain has shown more number of DEGs upon crude oil treatment in comparison to the other two strains. Through quantitative real time polymerase chain reaction (qRT-PCR), the selected DEGs of each strain from transcriptome data were substantiated. The results have shown that the up- regulated and down-regulated genes observed by qRT-PCR were consistent with transcriptome data. Taken together, our transcriptome results have revealed that TP16 is a potential P. aeruginosa strain for functional analysis of identified potential DEGs involved in crude oil degradation.
在微生物世界中，细菌是降解石油烃（PHs）、利用/矿化石油烃的最有效因子，它们是污染环境中原油的主要降解者。一些基因和特性参与了烃类的利用过程，因此对不同条件下的差异表达基因（DEGs）进行转录组分析对于了解与原油降解相关的基因或途径非常重要。在这项工作中，对三种利用原油的铜绿假单胞菌菌株 N002、TP16 和 J001 进行了转录组分析，共发现了 81、269 和 137 个显著的差异表达基因。其中，N002 有 80 个上调基因和 1 个下调基因，TP16 有 121 个上调基因和 148 个下调基因，J001 有 97 个上调基因和 40 个下调基因，这些基因参与了各种代谢途径。与其他两种菌株相比，TP16 菌株在受到原油处理时表现出更多数量的差异表达基因。通过定量实时聚合酶链反应（qRT-PCR），对转录组数据中各菌株的选定差异表达基因进行了验证。结果表明，qRT-PCR 观察到的上调和下调基因与转录组数据一致。总之，我们的转录组结果表明，TP16 是一株具有功能分析潜力的铜绿假单胞菌菌株，可用于研究与原油降解相关的潜在差异表达基因。
