Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA.
BMC Genomics. 2020 Mar 30;21(1):261. doi: 10.1186/s12864-020-6699-5.
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) ppGpp 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 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 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 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.
核苷酸第二信使，即鸟苷四磷酸和五磷酸[统称为(p)ppGpp]，在营养饥饿条件下触发严格反应，并在火疫病病原体欧文氏菌的毒力中发挥重要作用。在这里，我们进行了转录组分析，以揭示(p)ppGpp 介导的严格反应对欧文氏菌在诱导型三型分泌系统（T3SS）最小培养基（HMM）中的整体影响。
在这项研究中，我们使用 RNA-seq 研究了(p)ppGpp 突变体在 T3SS 诱导条件下的转录组变化。共发现了 1314 个差异表达基因（DEGs），占欧文氏菌基因组中所有基因的三分之一以上（36.8%）。与野生型相比，(p)ppGpp 突变体表现出参与肽 ATP 结合盒（ABC）转运体和毒力相关过程的基因下调，包括三型分泌系统（T3SS）、生物膜和运动性。有趣的是，与之前的报道相反，(p)ppGpp 突变体表现出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在欧文氏菌中是由(p)ppGpp 间接调节的，或者代表使用的特定培养条件。此外，(p)ppGpp 突变体还表现出参与翻译、SOS 反应、DNA 复制、染色体分离以及核苷酸、脂肪酸和脂质生物合成的基因上调。
这些发现表明，在 HMM 环境中，欧文氏菌可能将(p)ppGpp 用作激活毒力基因表达的信号，同时通过负调控 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来平衡毒力和生存。因此，(p)ppGpp 可能是开发针对这种毁灭性苹果和梨病害的新型控制措施的有前途的目标。
