RNA-seq transcriptome of Pseudomonas putida KT2440 fed with glucose as sole carbon source

Known for its biotechnological potential particularly in mediating environmental bioremediation, Pseudomonas putida KT2440 is a well-studied bacterium with varied habitats. With a genome encoding a versatile metabolism, the Gram-negative P. putida KT2440 can theoretically subsist on different carbon sources and remain efficient in performing desired biotechnological tasks. But, growth on different carbon sources would theoretically lead to different gene expression patterns that might ultimately impact on downstream metabolic activities and biotransformation tasks such as those required in environmental bioremediation. Hence, using a RNA-seq transcriptome of P. putida KT2440 subsisting on glucose as sole carbon source (ArrayExpress accession number: E-GEOD-46491), this work sought to reveal the differential gene expression pattern elicited by this preferred carbon source. After processing 0.7 million reads using an in-house MATLAB algorithm, the RNA-seq data reveals non-ribosomal peptide synthesis as major cellular processes in operation. In particular, the most highly expressed genes are pvdL, fliC, pvdD, pvdJ, groL, fpvA, pvdI, fusA, and pvdH, which was a surprise given that non-ribosomal peptide synthesis genes dominated the list of most highly expressed genes in cells at mid-exponential phase. More importantly, there was a paucity of genes inducible by glucose that top the list of most highly expressed genes, thereby, suggesting that enzymes mediating glucose catabolism are highly efficient molecular machines that do not need high expression level to afford high enzymatic activity. In summary, the presented RNA-seq transcriptome of P. putida KT2440 subsisting on glucose as sole carbon source might be useful in the search for differentially expressed genes when the same microbe subsists on different carbon sources such as fructose and glycerol.