Abstract
BackgroundPseudomonas syringae is an important plant pathogen, which could adapt many different environmental conditions. Under the nutrient-limited and other stress conditions, P. syringae produces nucleotide signal molecules, i.e., guanosine tetra/pentaphosphate ((p)ppGpp), to globally regulate gene expression. Previous studies showed that (p) ppGpp played an important role in regulating virulence factors in P. syringae pv. tomato DC3000 (PstDC3000) and P. syringae pv. syringae B728a (PssB728a). Here we present a comparative transcriptomic analysis to uncover the overall effects of (p)ppGpp-mediated stringent response in P. syringae.ResultsIn this study, we investigated global gene expression profiles of PstDC3000 and PssB728a and their corresponding (p)ppGpp0 mutants in hrp-inducing minimal medium (HMM) using RNA-seq. A total of 1886 and 1562 differentially expressed genes (DEGs) were uncovered between the (p)ppGpp0 mutants and the wild-type in PstDC3000 and PssB728a, respectively. Comparative transcriptomics identified 1613 common DEGs, as well as 444 and 293 unique DEGs in PstDC3000 and PssB728a, respectively. Functional cluster analysis revealed that (p) ppGpp positively regulated a variety of virulence-associated genes, including type III secretion system (T3SS), type VI secretion system (T6SS), cell motility, cell division, and alginate biosynthesis, while negatively regulated multiple basic physiological processes, including DNA replication, RNA processes, nucleotide biosynthesis, fatty acid metabolism, ribosome protein biosynthesis, and amino acid metabolism in both PstDC3000 and PssB728a. Furthermore, (p) ppGpp had divergent effects on other processes in PstDC3000 and PssB728a, including phytotoxin, nitrogen regulation and general secretion pathway (GSP).ConclusionIn this study, comparative transcriptomic analysis reveals common regulatory networks in both PstDC3000 and PssB728a mediated by (p) ppGpp in HMM. In both P. syringae systems, (p) ppGpp re-allocate cellular resources by suppressing multiple basic physiological activities and enhancing virulence gene expression, suggesting a balance between growth, survival and virulence. Our research is important in that due to similar global gene expression mediated by (p) ppGpp in both PstDC3000 and PssB728a, it is reasonable to propose that (p) ppGpp could be used as a target to develop novel control measures to fight against important plant bacterial diseases.
Highlights
Pseudomonas syringae is an important plant pathogen, which could adapt many different environmental conditions
We demonstrated that the stringent response mediated by (p) ppGpp plays a major role in virulence and survival in both PstDC3000 and PssB728a [26, 27]
11,261,275 to 23,836,829 reads for each biological sample were generated for PstDC3000 and its triple mutant ((p)ppGpp0PstDC3000), and the percentage of reads mapped to PstDC3000 genome ranged from 96.4 to 97.5%; whereas 13,562,836 to 22,961,086 reads for each biological sample were obtained for PssB728a and its double mutants ((p)ppGpp0PssB728a), and the percentage of reads mapped to PssB728a genome were from 96.8 to 97.3%
Summary
Pseudomonas syringae is an important plant pathogen, which could adapt many different environmental conditions. Under the nutrient-limited and other stress conditions, P. syringae produces nucleotide signal molecules, i.e., guanosine tetra/pentaphosphate ((p)ppGpp), to globally regulate gene expression. Previous studies showed that (p) ppGpp played an important role in regulating virulence factors in P. syringae pv. Pseudomonas syringae is a widely-distributed gram negative plant pathogenic bacterium, which can adapt many different environmental conditions, and cause diseases on many different host plants, including bean, cabbage, cucumber, tomato, tobacco and rice [1, 2]. Syringae (Pss) is the causal agent of brown spot on bean and an excellent epiphyte, which serves as a model system to study epiphytic fitness of pathogens on plant surfaces [6, 7]. The T3SS genes are rapidly induced under limited nutrition (minimal medium), low pH and relatively low temperature; and are induced in planta or by iron, but inhibited in rich medium [13, 14]
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