GEO DataSets

(Submitter supplied) Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24018

28 Samples

Download data: BED, TXT

(Submitter supplied) The model Gram-negative plant pathogen Pseudomonas syringae utilizes hundreds of transcription factors (TFs) to manipulate its functional processes, including virulence and metabolic pathways to control its infection to host plants. Although the molecular mechanisms of regulators have been studied for decades, the comprehensive understanding throughout the genome-wide TFs in P. syringae remains uncertain. more...

Organism:

Pseudomonas syringae pv. actinidiae str. Shaanxi_M228; Pseudomonas syringae pv. syringae B728a; Pseudomonas syringae pv. tomato str. DC3000; Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

396 Samples

Download data

(Submitter supplied) Bacteria relies on two-component systems (TCSs) to respond to a wide range of stimuli or environmental cues for their survival and virulence. However, the functions and synergistic actions of TCSs in genomic level remains unclear. Here, in model phytopathogen Pseudomonas syringae, by integrating multiomics data, we developed a network-based PSTCSome (Pseudomonas syringae two-component systems regulome) to identify functions and crosstalk among global TCSs under either virulence suppressing (King’s B medium, KB) or activating conditions (minimal medium, MM). more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24018

346 Samples

Download data: NARROWPEAK, XLSX

(Submitter supplied) Bacteria use a variety of mechanisms, such as two‐component regulatory systems (TCSs), to rapidly sense and respond to distinct conditions and signals in their host organisms. For example, a type III secretion system (T3SS) is the key determinant of the virulence of the model plant pathogen Pseudomonas syringae and contains the TCS RhpRS as a key regulator. However, the signal sensed by RhpRS remains unknown. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A; root metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL29322 GPL24018

48 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24018

148 Samples

Download data: BW, TXT

(Submitter supplied) The regulation of transcription is primarily exerted through transcription factors (TFs) binding to genomic DNA. Although molecular mechanisms of TFs have been studied individually for decades, a complete picture of binding profiles of all TFs and their precise targets in the genome are still lacking in the model pathogen Pseudomonas syringae. To this end, we performed a high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX) approach on all 301 annotated TFs in P. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL28310 GPL28245

513 Samples

Download data: TXT, XLS

(Submitter supplied) Lon protease plays vital roles in many biological processes in Pseudomonas syringae, including type III secretion systems (T3SS), transcription regulation, protein synthesis and energy metabolism. Lon also functions as a transcriptional regulator in other bacterial species (e.g., Escherichia coli and Brevibacillus thermoruber). Therefore, we hypothesise that Lon has dual functions in P. syringae. To reveal the molecular mechanisms of Lon as a transcriptional regulator and protease under different environmental conditions, we used a combination of transcriptome sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the genes or proteins regulated by Lon. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24018

12 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) Pseudomonas syringae, the leading cause of crop diseases world-wide, uses type III secretion system (T3SS) to invade host plants. Our previous studies demonstrate that two-component system RhpRS enable P. syringae to coordinate T3SS gene expression, which is dependent on the phosphorylation state of RhpR in different environmental conditions. Homologs of RhpRS are distributed in a wide range of bacterial species, indicating a general regulatory mechanism. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24018

26 Samples

Download data: XLSX

(Submitter supplied) 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. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24018

8 Samples

Download data: XLS

(Submitter supplied) Pseudomonas syringae uses two-component system RhpRS to regulate the expression of type III secretion system (T3SS) genes and bacterial virulence. However, the molecular mechanism and the regulons of RhpRS have yet to be fully elucidated. Here we show that RhpS functions as an autokinase, an RhpR kinase, and a P-RhpR phosphatase. RhpR can also be phosphorylated by small phosphodonor acetyl phosphate. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18810

4 Samples

Download data: TXT

(Submitter supplied) P. syringae pv. phaseolicola, the causal agent of halo blight disease in bean, produces a toxin known as phaseolotoxin, whose synthesis involves the product of some of the genes found within the Pht region. This region, considered a pathogenicity island, comprises 23 genes arranged in five transcriptional units; two single-gene units (argK, phtL) and three arranged as operons (phtA, phtD, phtM), most with unknown function. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Expression profiling by array

Platform:

GPL7115

6 Samples

Download data: GPR, TXT

(Submitter supplied) In order to obtain a global view about the strategies used by phytopathogenic bacteria, in response to physiologically relevant temperature changes. We used the DNA microarray technology to compare gene expression profile in the model bacterial pathogen P. syringae pv. phaseolicola NPS3121 grown at 18 ºC and 28ºC.

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Expression profiling by array

Platform:

GPL7115

6 Samples

Download data: GPR

(Submitter supplied) Pseudomonas syringae pv. phaseolicola is the causal agent of halo blight disease of beans (Phaseolus vulgaris L.), which is characterized by water-soaked lesions surrounded by a chlorotic halo resulting from the action of a non-host-specific toxin known as phaseolotoxin, that inhibits the enzyme ornithine carbamoyltransferase involved in the arginine biosynthesis pathway. It was previously reported that genes within the Pht cluster were involved in the regulation and synthesis of phaseolotoxin. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Expression profiling by array

Platform:

GPL7115

6 Samples

Download data: GPR

(Submitter supplied) Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. Bean leaf extract was obtained from healthy bean leaves. In this work we investigated the effect of bean leaf extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without extract from healthy bean leaves.

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Expression profiling by array

Platform:

GPL7115

6 Samples

Download data: GPR

(Submitter supplied) Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. Plant apoplast is the primary site of infection for P. syringae, which obtain nutrients directly from apoplastic fluid of host plants. In this work we investigated the effect of apoplastic fluid on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without apoplastic fluid extracted from healthy bean leaves. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Expression profiling by array

Platform:

GPL7115

6 Samples

Download data: GPR

(Submitter supplied) P. syringae pv. phaseolicola is the causal agent of the halo blight disease of beans (Phaseolus vulgaris L). The disease attacks both foliage and pods of plant host. Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. In this work we investigated the effect of bean pod extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without bean pod extract.

Organism:

Pseudomonas savastanoi pv. phaseolicola

Type:

Expression profiling by array

Platform:

GPL7115

6 Samples

Download data: GPR