Diversity of HrpL-regulons across Pseudomonas syringae isolates
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ABSTRACT:
ORGANISM(S): Pseudomonas syringae
PROVIDER: GSE46930 | GEO | 2014/01/01
SECONDARY ACCESSION(S): PRJNA203106
REPOSITORIES: GEO
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Project description:We implemented transcriptional analysis methods using cDNA and high-throughput sequencing data to identify HrpL-regulated genes for six strains of Pseudomonas syringae Each Pseudomonas syringae strains was transformed with either pBAD::EV or pBAD containing native hrpL sequence. Strains were grown in MM media supplemented with arabinose and collected 1, 3, and 5 hours post arabinose treatment. RNA was extracted for each time point and mixed at a 1/3 ratio. After removal of rRNA, double stranded cDNA was generated and library prepared accordeing to Illumina protocols.
2014-01-01 | E-GEOD-46930 | biostudies-arrayexpress
Project description:Pseudomonas syringae, a Gram-negative plant pathogen, infects more than 50 crops with its type III secretion system (T3SS) and causes severe economic losses around the world. Although the mechanisms of virulence-associated regulators of P. syringae T3SS have been studied for decades, the crosstalk and network underlying these regulators are still elusive. Previously, we have individually studied a group of T3SS regulators, including AefR, HrpS, and RhpRS. In the present study, we found 4 new T3SS regulator genes (envZ, ompR, tsiS and phoQ) via transposon-mediated mutagenesis. Two-component systems EnvZ and TsiS natively regulate T3SS. In order to uncover the crosstalk between 16 virulence-associated regulators, (including AefR, AlgU, CvsR, GacA, HrpL, HrpR, HrpS, MgrA, OmpR, PhoP, PilR, PsrA, RhpR, RpoN, TsiR and Vfr) in P. syringae, we mapped an intricate network named PSVnet (Pseudomonas syringae Virulence Regulatory Network) by combining differentially expression genes in RNA-seq and binding loci in ChIP-seq of all regulators.
2021-03-29 | GSE138204 | GEO
Project description:The type III secretion system (T3SS) is the main machinery for Pseudomonas syringae and other Gram-negative bacteria to invade plant cells. HrpR/HrpS heterodimer are key factors to activate HrpL which induces all T3SS genes by binding to a ‘hrp box’ in promoters. However, the molecular mechanisms of HrpRS on T3SS or non-T3SS genes have not been fully understood. Following by chromatin immunoprecipitation coupled to high-throughput DNA sequencing (ChIP-seq), we found that HrpRSL had 8, 38, and 36 targets on the genome, respectively. HrpS directly bound to the promoter regions of T3SS genes (hrpK1, hrpA2 and hopAJ1) as well as a group of non-T3SS genes (PSPPH_1496, PSPPH_1525, PSPPH_3494 and PSPPH_3495). Subsequent biochemical and genetic assays showed that HrpS independently regulated these genes in a hrpL deletion strain. In addition, a HrpS-binding motif (GTGCCAAA) in the hrpL promoter was identified by truncation, which was verified by EMSA in vitro and lux-reporter assay in vivo. On the contrary, HrpR alone couldn’t activate hrpL. Overall, our results demonstrated that HrpS directly regulated a group of T3SS and non-T3SS genes, which is independent on HrpL. HrpS functions as the center of the regulatory cascade in T3SS. This work deciphered the key HrpRSL-T3SS regulatory network, which provides insights to develop new strategies to control P. syringae infection in the future.
2018-06-30 | GSE103921 | GEO
Project description:Diversity of HrpL-regulons across Pseudomonas syringae isolates
| PRJNA203106 | ENA
Project description:Pseudomonas syringae pv. tomato DC3000 is a model pathogen infecting tomato and Arabidopsis plants. Genes encoding the type III secretion system and substrate proteins (collectively called TTSS genes) of this bacterium are induced in plants and in minimal medium (MM). The induction of TTSS genes is mediated by HrpL, an alternative sigma factor recognizing the hrp box in the promoter of TTSS genes. The transcription of hrpL is activated by HrpR and HrpS, two homologous DNA binding proteins encoded by the hrpRS operon. Microarray analysis was conducted to evaluate the DC3000 genes regulated by hrpL and hrpRS in MM. The analysis identified a number of novel hrpLactivated genes with a putative TTSS-independent function. Genes regulated by hrpL were mostly regulated by hrpRS in the same manner, but a large number of genes regulated by hrpRS were hrpL-independent, indicating that hrpL represents one branch of the regulatory pathways downstream of hrpRS. The induction of the TTSS genes was associated with down-regulation of the house-keeping genes, indicating that the activation of the TTSS has a cost on the basic cellular activities. The novel genes/pathways identified by the microarray provide new insight into the bacterial functions coordinating with the TTSS.
2006-08-01 | GSE4848 | GEO
Project description:The plant pathogen Pseudomonas syringae pv. syringae B728a grows and survives on leaf surfaces and in the leaf apoplast of its host, bean. Global transcriptome profiling was used to understand the contribution of distinct regulators to B728a fitness and pathogenicity. We performed a transcriptome analysis of B728a and nine regulator mutants recovered from the surface and interior of leaves and exposed to various environmental stresses in culture. These mutants were nonpolar deletion mutants lacking a single target regulator gene: ahlR, aefR, gacS, retS, salA, rpoS, algU, hrpL and rpoN. RNA was collected from cells of these strains that were exposed to five treatments in vitro, namely a basal medium, sodium chloride to confer an osmotic stress, hydrogen peroxide to confer an oxidative stress, iron limitation, and nitrogen limitation, and were recovered from two bean (Phaseolus vulgaris L.) leaf sites, namely epiphytic sites after leaf surface inoculation and 72 h of growth and apoplastic sites after leaf infiltration and 48 h of growth. The results indicated that the quorum-sensing regulators AhlR and AefR influenced few genes in planta or in vitro. In contrast, GacS and a downstream regulator SalA formed a large regulatory network that included a branch that regulated diverse traits and was independent of plant-specific environmental signals, and a signal-dependent branch that positively regulated secondary metabolite genes and negatively regulated the type III secretion system. RetS functioned almost exclusively to repress secondary metabolite genes in cells in culture but not on leaves. SalA functioned as a central regulator of iron status, based on its reciprocal regulation of pyoverdine and achromobactin genes, and also sulfur uptake, suggesting a role in the iron-sulfur balance. Among the sigma factors examined, AlgU influenced many more genes than RpoS, and most AlgU-regulated genes depended on RpoN. RpoN differentially impacted many AlgU- and GacS-activated genes in cells recovered from apoplastic versus epiphytic sites, suggesting differences in environmental signals or bacterial stress status in these two habitats. Collectively, our findings illustrate a central role for GacS, SalA, RpoN and AlgU in global regulation in B728a in planta and a high level of plasticity in their response to distinct environmental signals.
2014-09-01 | GSE59273 | GEO
Project description:A ChIP-seq assay was performed to identify the regulons of an ompR-like transcription factor (gene name: 13375, GenBank: AYL80818.1) in Pseudomonas syringae pv. actinidiae. An 13375-overexpressing mutant G1-OE13375, which constitutively express C-terminally Myc-tagged ompR-like gene in the 13375-deletion mutant G1Δ13375, was used in this study. The bacterial cells were cultured either in nutrition-rich KB medium or hrp-derepressing medium (HDM) at 25 C for 24 hours. A PierceTM Magnetic ChIP Kit (Cat. #: 26157, Thermo Fisher Scientific) and a ChIP-grade Myc-Tag Monoclonal Antibody (Myc.A7, Cat. #: MA121316, Thermo Fisher Scientific) were used for sample pretreatment and immunoprecipitation.
2022-12-13 | GSE220275 | GEO
Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level.
2013-06-01 | GSE39246 | GEO
Project description:Pseudomonas syringae pv. syringae 9644 (Pss9644) is a causal agent of bacterial cherry canker causing necrotic symptoms on leaves, fruits, gummosis and canker in woody tissues of sweet cherry (Prunus avium). To understand which virulent factor genes were expressed in vitro, Pss9644 was grown in rich media (King's B Broth) and minimum media (hrp-inducing minimum media). The latter mimics the in planta environment.
2024-04-07 | GSE255102 | GEO
Project description:The effect of bacterial infection with Pseudomonas syringae on gene expression of Arabidopsis thaliana
2005-01-01 | E-TIGR-3 | biostudies-arrayexpress