Multidimensional gene regulatory landscape of a bacterial pathogen in plants

Understanding the gene regulation of plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a bacterial pathogen in plants. We found a number of bacterial processes affected by plant immunity at the transcriptome and proteome levels. For instance, the salicylic acid-mediated plant immunity suppressed the accumulation of proteins comprising the tip component of bacterial type III secretion system. Interestingly, there were instances of concordant and discordant regulation of bacterial mRNAs and proteins. Gene co-expression analysis uncovered previously unknown gene regulatory modules underlying virulence. This study provides molecular insights into the multiple layers of gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in affecting pathogen responses. Transcriptomes of P. syringae pv. tomato DC3000 during infection to four Arabidopsis thaliana genotypes. Bacterial suspension was syringe infiltrated to plant leaves at OD600=0.005. At 48 h after infection, the infected leaves were harvested and bacterial cells were isolated, followed by RNA extraction. Ribosomal RNA of bacteria and plants were removed with a commercial kit to enrich bacterial mRNA. Then, cDNA libraries were generated and RNA-Seq was performed. For each condition, three independent replicates were taken.