RNA-seq reveals quorum sensing-dependent activation of genes involved in ecological fitness during Pcb1692 potato-host infection

Pectobacterium carotovorum subsp. brasiliense 1692 (Pcb1692) is an emerging pathogen of significance affecting potato production globally. In the current study, we reveal the complete transcriptome of Pcb in planta at the early and later stages of infection (24 and 72 hour post inoculation (hpi), respectively) using RNA-seq. We identified713 differentially expressed genes at 24hpi and an additional 157 differentially expressed genes at 72 hpi. Genes encoding PCWDEs and iron acquisition were up-regulated. The type VI secretion system (T6SS) and the bacteriocin (carotovoricin) gene clusters were both highly up-regulated, suggesting they might play a role in antibacterial activity in eliminating competition for nutrients with other microbes within the niche. Additionally, our results suggest the importance of genes involved in amino acid, carbohydrates, citrate metabolism, adhesion, chemotaxis, motility, metabolism as these were differentially expressed at 24 hpi. To establish the Pcb1692 quorum sensing regulon, the transcriptome of Pcb1692 wild-type compared to that of Pcb1692?expI during in vitro growth and in planta at 24 hpi in potato tubers was analyzed. Important virulence factors such as T2SS, T6SS, and citrate metabolism were found to be under quorum sensing regulation while, carotovoricin did not appear to be quorum sensing dependent. Overall design: Examination of Pcb 1692 gene expression in potato tuber at 24 and 72 hpi. Additionally, the transcriptome of Pcb1692 wild-type was compared to that of Pcb1692?expI during in vitro growth and in planta at 24 hpi in potato tubers