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

Glycerol is a potential carbon source for the cultivation of various bacterial species given the presence of metabolic pathways for its catabolism. But, its use lags behind the preferred carbon source, glucose. However, glycerol is increasingly being produced as a byproduct in biodiesel production, and thus, efforts have been expended in exploring the use of glycerol as carbon source in support of microbial fermentation. This work hopes to make a contribution in this direction by analysing the RNA-seq transcriptome of Pseudomonas putida KT2440 (ArrayExpress accession number: E-GEOD-46491) cultivated with glycerol as sole carbon source. Although P. putida KT2440 is commonly used in environmental remediation as opposed to biotechnology, it nevertheless might inform the metabolism of glycerol given the versatile metabolism encoded by a relatively large genome. Buttressed by a dataset comprising 0.7 million reads, the RNA-seq transcriptome of P. putida KT2440 showed a preponderance of non-ribosomal peptide synthesis enzymes being highly expressed together with cell surface proteins. High expression of non-ribosomal peptide synthetase is unusual given that RNA was extracted from cells in the mid-exponential phase. In total, the most highly expressed genes were: non-ribosomal peptide synthetase pvdL, surface adhesion protein, putative surface adhesion protein, quinoprotein ethanol dehydrogenase qedH-I, non-ribosomal peptide synthetase pvdD, aldehyde dehydrogenase aldB-II, diaminobutyrate-2-oxoglutarate transaminase pvdH, ribosome modulation factor rmf, non-ribosomal peptide synthetase pvdJ, and L-ornithine 5-monooxygenase pvdA. Overall, much remains to be deciphered from the RNA-seq transcriptome of P. putida KT2440 utilising glycerol as sole carbon source. Even though P. putida KT2440 is not a microbial cell factory, its gene expression pattern while utilising glycerol may still offer clues to the activation of specific branches of central carbon metabolism that have not been observed to date.