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Background  The nucleotide second messengers, i.e., guanosine tetraphosphate and pentaphosphate [collectively referred to as (p) ppGpp], trigger the stringent response under nutrient starvation conditions and play an essential role in virulence in the fire blight pathogen  Erwinia amylovora . Here, we present transcriptomic analyses to uncover the overall effect of (p) ppGpp-mediated stringent response in  E. amylovora  in the  hrp -inducing minimal medium (HMM).    Results  In this study, we investigated the transcriptomic changes of the (p) ppGpp 0  mutant under the type III secretion system (T3SS)-inducing condition using RNA-seq. A total of 1314 differentially expressed genes (DEGs) was uncovered, representing more than one third (36.8%) of all genes in the  E. amylovora  genome. Compared to the wild-type, the (p) ppGpp 0  mutant showed down-regulation of genes involved in peptide ATP-binding cassette (ABC) transporters and virulence-related processes, including type III secretion system (T3SS), biofilm, and motility. Interestingly, in contrast to previous reports, the (p) ppGpp 0  mutant showed up-regulation of amino acid biosynthesis genes, suggesting that it might be due to that these amino acid biosynthesis genes are indirectly regulated by (p) ppGpp in  E. amylovora  or represent specific culturing condition used. Furthermore, the (p) ppGpp 0  mutant exhibited up-regulation of genes involved in translation, SOS response, DNA replication, chromosome segregation, as well as biosynthesis of nucleotide, fatty acid and lipid.    Conclusion  These findings suggested that in HMM environment,  E. amylovora  might use (p) ppGpp as a signal to activate virulence gene expression, and simultaneously mediate the balance between virulence and survival by negatively regulating DNA replication, translation, cell division, as well as biosynthesis of nucleotide, amino acid, fatty acid, and lipid. Therefore, (p) ppGpp could be a promising target for developing novel control measures to fight against this devastating disease of apples and pears.

The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora