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.