Comparative transcriptomic analysis of global gene expression mediated by (p) ppGpp reveals common regulatory networks in Pseudomonas syringae
| Autor: | Tiyakhon Chatnaparat, Jae Hoon Lee, Baishi Hu, Menghao Yu, Youfu Zhao, Yanli Tian, Jun Liu |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
lcsh:QH426-470
Stringent response lcsh:Biotechnology Mutant Virulence Pseudomonas syringae Biology DC3000 Type three secretion system 03 medical and health sciences Bacterial Proteins Solanum lycopersicum lcsh:TP248.13-248.65 Gene expression Exome Sequencing Genetics Cluster Analysis Gene Regulatory Networks Gene 030304 developmental biology Type VI secretion system Plant Diseases 0303 health sciences Virulence factors 030306 microbiology Sequence Analysis RNA Gene Expression Profiling Guanosine Pentaphosphate Secondary messenger Gene Expression Regulation Bacterial lcsh:Genetics B728a RNA-seq Biotechnology Research Article |
| Zdroj: | BMC Genomics BMC Genomics, Vol 21, Iss 1, Pp 1-18 (2020) |
| ISSN: | 1471-2164 |
| Popis: | 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 (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. Results In this study, we investigated global gene expression profiles of PstDC3000 and PssB728a and their corresponding (p)ppGpp0 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)ppGpp0 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). Conclusion 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. |
| Databáze: | OpenAIRE |
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