Transcriptomic analysis of the Pseudomonas sp. AP3_22 exposed to the sodium dodecyl sulfate

Here we presented the detailed transcriptomic analysis for Pseudomonas sp. AP3_22, an effective sodium dodecyl sulfate degrader isolated from the soil sample from wastewater treatment plant, cultured in the presence of SDS to get the first insight in the global bacterial response toward Sthis anionic detergent. Our results suggest showed that although SDS could be used as a carbon source, in the first place it acts influence on integrity of the cell envelopes and causes global stress response together combined with cell wall modification and repair induction. These results suggest that the modulation of the membrane content composition is first adaptation step in a typical response to detergent exposure. As the second response to the sodium dodecyl sulfate the AP3_22 strain metabolism was shifted from the lipid biosynthesis to the lipid catabolism and the SDS degradation started. Overall design: AP3_22 strain was precultured overnight in LB medium. Then washed with minimal medium and diluted in the fresh 0.1 LB medium with or without (the control sample) SDS (5 g/L) to the initial OD600=0.4 and cultured in 30°C with 140 rpm agitation. The samples for RNA isolation were collected at following time points: at the beginning (0 minutes) and after: 30 minutes; 60 minutes; and 150 minutes of the experiment. The experiment was made in triplicate (three biological replicates for control and three biological replicates for the sample).

本研究针对从污水处理厂土壤样品中分离得到的高效十二烷基硫酸钠（sodium dodecyl sulfate, SDS）降解菌——假单胞菌属（Pseudomonas sp.）AP3_22菌株，开展了详细的转录组分析（transcriptomic analysis）；通过在添加SDS的条件下培养该菌株，首次解析其应对该阴离子去污剂的全局细菌应答机制。本研究结果显示，尽管SDS可作为碳源被该菌株利用，但首先会破坏细菌细胞膜完整性，并引发全局应激反应，伴随细胞壁修饰与修复的诱导。上述结果表明，膜组分组成的调控是细菌应对去污剂暴露的典型适应性响应的首要步骤。针对SDS的第二重应答中，AP3_22菌株的代谢从脂质生物合成转向脂质分解代谢，并启动SDS降解过程。实验设计：将AP3_22菌株于LB培养基中过夜预培养，随后用基础培养基（minimal medium）洗涤并重悬，稀释至初始OD600=0.4后，接种于添加或不添加（对照组）5 g/L SDS的新鲜0.1倍LB培养基中，于30℃、140 rpm振荡条件下培养。分别于实验起始（0分钟）及30、60、150分钟四个时间点收集用于RNA提取的样品。本实验设置三次生物学重复（biological replicate），对照组与处理组各3次生物学重复。