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). In this study, we investigated the transcriptomic changes of the (p) ppGpp0 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) ppGpp0 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) ppGpp0 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) ppGpp0 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. 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.

中文翻译：

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严格的应答调节因子（p）ppGpp介导了解淀粉欧文氏菌中的毒力基因表达和存活

核苷酸第二信使，即鸟嘌呤四磷酸和五磷酸[统称为（p）ppGpp]，在营养饥饿的条件下触发严格的反应，并在火疫病病原体小球藻欧文氏菌的毒力中起重要作用。在这里，我们介绍了转录组学分析，以揭示在hrp诱导基本培养基（HMM）中的（p）ppGpp介导的淀粉样芽胞杆菌严格反应的总体效果。在这项研究中，我们调查了使用RNA序列在III型分泌系统（T3SS）诱导条件下（p）ppGpp0突变体的转录组变化。总共发现了1314个差异表达基因（DEGs），占Emy Amylovora基因组中所有基因的三分之一以上（36.8％）。与野生型相比，（p）ppGpp0突变体显示参与肽ATP结合盒（ABC）转运蛋白和毒力相关过程的基因下调，包括III型分泌系统（T3SS），生物膜和运动性。有趣的是，与以前的报道相反，（p）ppGpp0突变体显示了氨基酸生物合成基因的上调，这表明这可能是由于这些氨基酸生物合成基因被（p）ppGpp间接调控的。代表所使用的特定培养条件。此外，（p）ppGpp0突变体表现出与翻译，SOS反应，DNA复制，染色体分离以及核苷酸，脂肪酸和脂质的生物合成有关的基因上调。这些发现表明，在HMM环境中，支链淀粉菌可能会使用（p）ppGpp作为激活毒力基因表达的信号，通过负调控DNA复制，翻译，细胞分裂以及核苷酸，氨基酸，脂肪酸和脂质的生物合成，同时介导毒力和存活之间的平衡。因此，（p）ppGpp可能成为开发新颖的控制措施来对抗这种破坏性的苹果和梨病的有希望的目标。