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Background   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.  tomato  DC3000 ( Pst DC3000) and  P. syringae  pv.  syringae  B728a ( Pss B728a). Here we present a comparative transcriptomic analysis to uncover the overall effects of (p)ppGpp-mediated stringent response in  P. syringae .    Results  In this study, we investigated global gene expression profiles of  Pst DC3000 and  Pss B728a and their corresponding (p)ppGpp 0  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)ppGpp 0  mutants and the wild-type in  Pst DC3000 and  Pss B728a, respectively. Comparative transcriptomics identified 1613 common DEGs, as well as 444 and 293 unique DEGs in  Pst DC3000 and  Pss B728a, 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  Pst DC3000 and  Pss B728a. Furthermore, (p) ppGpp had divergent effects on other processes in  Pst DC3000 and  Pss B728a, including phytotoxin, nitrogen regulation and general secretion pathway (GSP).    Conclusion  In this study, comparative transcriptomic analysis reveals common regulatory networks in both  Pst DC3000 and  Pss B728a 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  Pst DC3000 and  Pss B728a, 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.

Comparative transcriptomic analysis of global gene expression mediated by (p) ppGpp reveals common regulatory networks in Pseudomonas syringae