College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, 210095, P. R. China.
Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL, 61801, USA.
BMC Genomics. 2020 Apr 10;21(1):296. doi: 10.1186/s12864-020-6701-2.
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 (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.
In this study, we investigated global gene expression profiles of PstDC3000 and PssB728a and their corresponding (p)ppGpp 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 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).
In 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.
丁香假单胞菌是一种重要的植物病原体，能够适应许多不同的环境条件。在营养有限和其他胁迫条件下，丁香假单胞菌会产生核苷酸信号分子，即鸟苷四/五磷酸((p)ppGpp)，以全局调控基因表达。先前的研究表明，(p)ppGpp 在调控丁香假单胞菌 pv.番茄 DC3000（PstDC3000）和丁香假单胞菌 pv.丁香致病变种 B728a（PssB728a）中的毒力因子方面发挥着重要作用。在这里，我们进行了比较转录组分析，以揭示 (p)ppGpp 介导的严格反应在丁香假单胞菌中的整体效应。
在这项研究中，我们使用 RNA-seq 研究了 PstDC3000 和 PssB728a 及其相应的 (p)ppGpp 突变体在诱导性最小培养基（HMM）中的全局基因表达谱。在 PstDC3000 和 PssB728a 中，(p)ppGpp 突变体与野生型之间分别发现了 1886 和 1562 个差异表达基因（DEG）。比较转录组学鉴定了 1613 个共同的 DEG，以及 PstDC3000 和 PssB728a 中分别有 444 和 293 个独特的 DEG。功能聚类分析表明，(p)ppGpp 正向调控多种与毒力相关的基因，包括 III 型分泌系统（T3SS）、VI 型分泌系统（T6SS）、细胞运动、细胞分裂和海藻酸盐生物合成，而在 PstDC3000 和 PssB728a 中，(p)ppGpp 则负调控多种基本生理过程，包括 DNA 复制、RNA 过程、核苷酸生物合成、脂肪酸代谢、核糖体蛋白生物合成和氨基酸代谢。此外，(p)ppGpp 在 PstDC3000 和 PssB728a 中对其他过程的影响也存在差异，包括植物毒素、氮调控和一般分泌途径（GSP）。
在这项研究中，比较转录组学分析揭示了在 HMM 中，(p)ppGpp 在 PstDC3000 和 PssB728a 中介导的共同调控网络。在这两个丁香假单胞菌系统中，(p)ppGpp 通过抑制多种基本生理活动和增强毒力基因表达来重新分配细胞资源，这表明生长、存活和毒力之间存在平衡。我们的研究很重要，因为由于 (p)ppGpp 在 PstDC3000 和 PssB728a 中介导的全局基因表达相似，因此可以合理地提出，(p)ppGpp 可以作为一个靶点，开发新的控制措施来对抗重要的植物细菌性疾病。
