RNA-seq transcriptome of Pseudomonas syringae DC3000 in liquid minimal medium

Known as a plant pathogen able to infect a multitude of plant species, Pseudomonas syringae is attracting much research interest from the plant biology community, particularly with respect to the development of methods for preventing P. syringae infection, and understanding its pathogenesis mechanisms. This work presents an analysis of the RNA-seq transcriptome of P. syringae DC3000 in liquid minimal medium (ArrayExpress accession number: E-MTAB-3779). Analysed by an in-house MATLAB transcriptome analysis software, RNA-seq transcriptome of P. syringae’s growth in liquid minimal medium holds biological relevance given the oligotrophic nature of plant surfaces on which this bacterium thrives and exerts its pathogenetic effects. Through processing 1.5 million reads, the transcriptional picture reveals a set of highly transcribed genes that include outer membrane porin OprF, molecular chaperone DnaK, groEL chaperonin, fliC flagellin, ISPsy5 transposase, pyoverdine chromophore precursor synthetase, RNA polymerase sigma factor SigX, yersiniabactin polyketide/non-ribosomal peptide, and heat shock protein HtpG. Such a gene expression programme speaks of the importance of maintaining the cell envelope as well as protein conformational fidelity to the proper functioning of the cell. In addition, high level expression of the transposase genes as well as other transposase helper proteins point to a source of genetic instability in the species, which may have ramifications on the species pathogenicity. Overall, the RNA-seq transcriptome of P. syringae DC3000 reveals that the cell expends significant resources to maintain proper protein folding and the integrity of the cell envelope. But, the transcriptome also highlights one area in which CRISPR-Cas9 might help in reducing genetic instability of the bacterium that otherwise aids the species in evading plant host’s immune system. In essence, transposase genes can be candidate genes to be inactivated to help reduce pathogenicity potential of this plant pathogen.