A computational model of Pseudomonas syringae metabolism unveils the role of branched-chain amino acids in virulence expression at the early stages of Arabidopsis colonization

Leaf mesophyll-colonizing bacterial pathogens infect their plant hosts by adjusting their metabolism to the leaf mesophyll environment. Soon after the inoculation of naïve, susceptible plants, the model bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (PstDC3000) expresses virulence factors that suppress plant immunity, a requirement to produce robust infections. However, if plant immunity was elicited with Microbe-Associated Molecular-Patterns (MAMPs) prior to bacterial inoculation, PstDC3000 slows down virulence expression and only produces symptomless mild infections. To understand how bacterial metabolism adapts to these two contrasting conditions, we created iPst19, an in silico ensemble of genome-scale metabolic reconstructions. Constraining the in silico growth of iPst19 with in planta PstDC3000 gene expression data revealed that sugar catabolism is highly active in bacteria that have been inoculated in mock-treated plants. In contrast, branched-chain amino acids (BCAAs) catabolism is highly active in bacteria that have been inoculated in MAMP-pretreated plants. Bacterial growth and gene expression analysis showed that BCAAs suppress virulence gene expression without affecting bacterial growth in vitro. In planta, however, BCAAs suppress the expression of virulence genes at the early stages of the infection and significantly impair leaf colonization of the host plant Arabidopsis thaliana. While the overexpression of the conserved bacterial leucine-responsive transcriptional regulator Lrp induced the expression of virulence genes, its downregulation had the opposite effect, suggesting that BCAA-free Lrp induces virulence while BCAA-Lrp does not. Overall, our data provide mechanistic connections to understand how plant immunity impacts PstDC3000 metabolism and virulence, furthering our understanding of bacterial pathogenesis and plant disease.