RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on fructose as sole carbon source

Fructose is a metabolizable sugar that is able to tap on central carbon metabolism for its catabolism. But, fructose is not commonly used as a substrate for cultivating cells in biotechnology applications. In this contribution, the RNA-seq of Pseudomonas putida KT2440 (ArrayExpress accession number: E-GEOD-46491) subsisting on fructose as sole carbon source was analysed by an in-house MATLAB transcriptome analysis software. A total of 0.7 million reads were analysed, and the resulting transcriptome paints a picture of a cell devoting significant metabolic resources in expressing cell surface proteins. Specifically, the highly expressed genes were: putative surface adhesion protein, surface adhesion protein, ribosome modulation factor, quinoprotein ethanol dehydrogenase, flagellin, porin F, major outer membrane lipoprotein, non-ribosomal peptide synthetase, and basic amino acid specific porin OprD. High expression level of a fructose transporter, PTS fructose transporter subunit EI/HPr/IIA, fruB, indicated that P. putida KT2440 could sense presence of fructose, and activate a differential gene expression programme centred around the fructose regulon. Overall, the RNA-seq transcriptome presented in this work should find use in fundamental biology studies seeking to understand bacterial fructose metabolism in general, and how P. putida KT2440 uses this non-conventional sugar in particular.

果糖是一种可代谢糖类，其分解代谢可通过中心碳代谢途径完成。但在生物技术领域的细胞培养应用中，果糖并非常用的碳源底物。本研究采用自研MATLAB转录组分析软件，对以果糖为唯一碳源生长的恶臭假单胞菌KT2440（Pseudomonas putida KT2440）的RNA测序（RNA-seq）数据进行分析，该数据集的ArrayExpress登录号为E-GEOD-46491。本次分析共处理70万条测序读段，所得转录组数据显示，该菌株将大量代谢资源用于表达细胞表面蛋白。具体而言，高表达的基因包括：推定的表面黏附蛋白、表面黏附蛋白、核糖体调节因子、醌蛋白乙醇脱氢酶、鞭毛蛋白、孔蛋白F、主要外膜脂蛋白、非核糖体肽合成酶以及碱性氨基酸特异性孔蛋白OprD。果糖转运蛋白PTS果糖转运亚基EI/HPr/IIA（fruB）的高表达，表明恶臭假单胞菌KT2440可感知果糖的存在，并激活以果糖调控子为核心的差异基因表达程序。综上，本研究提供的RNA-seq转录组数据，可用于开展基础生物学研究，以全面解析细菌的果糖代谢机制，尤其可用于阐明恶臭假单胞菌KT2440对这类非常规糖类的利用方式。