GEO DataSets

(Submitter supplied) Pseudomonas syringae is an important plant pathogen that infects a wide variety of crops. The mgo (mangotoxin-generating operon) gene cluster produces an extracellular signaling molecule, leudiazen, and is highly conserved in Pseudomonas syringae strains. Here, we genetically removed mgo in Pseudomonas syringae pv. syringae (Pss) UMAF0158 to interrogate its impacts on bacterial infection. Loss of mgo not only alleviated the chlorosis symptom caused by Pss UMAF0158 infection, but also reduced bacterial population in tomato leaflets. more...

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 Samples

Download data: TXT

(Submitter supplied) Plant pathogenic bacteria encounter a drastic increase in apoplastic pH during the early stages of plant immunity. The effects of alkalization on pathogen-host interactions have not been comprehensively characterized. Here we used a global transcriptomic approach to assess the impact of environmental alkalization on Pseudomonas syringae pv. tomato DC3000 in vitro. In addition to the Type 3 Secretion System (T3SS), we found expression of genes encoding other virulence factors such as iron uptake, and coronatine biosynthesis to be strongly affected by environmental alkalization. more...

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34917

18 Samples

Download data: TXT

(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) 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.

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 Samples

Download data: TXT

(Submitter supplied) GacS/GacA is a widely distributed two-component system playing an essential role as a key global regulator, although its characterization in phytopathogenic bacteria has been deeply biased, being intensively studied in pathogens of herbaceous plants but barely investigated in pathogens of woody hosts. P. savastanoi pv. savastanoi (Psv) is characterized by inducing tumours in the stem and branches of olive trees. more...

Organism:

Pseudomonas savastanoi pv. savastanoi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34126

8 Samples

Download data: TXT

(Submitter supplied) The ecological significance of light perception in non-phototrophic bacteria remains largely elusive. In terrestrial environments, diurnal oscillations in light are often temporally coupled to other environmental changes, including increased temperature and evaporation. Here we report that light functions as an anticipatory cue that triggers protective adaptations to tolerate a future rapid loss of environmental water in leaf-associated Pseudomonas syringae pv. more...

Organism:

Pseudomonas syringae pv. syringae B728a

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29146

66 Samples

Download data: CSV, XLSX

(Submitter supplied) We sought to compare and contrast plant host and bacterial transcriptional changes during compatible infections that cause disease (albeit within different symptoms). We investigated the infection by the two Pseudomonas syringae sensu lato strains P. syringae pv. syringae B728a (Psy) and P. amygdali pv. tabaci 11528 (Pta) of Nicotiana benthamiana at an early time point post inoculation to understand how a plant host responds to two related bacteria with different infection strategies. more...

Organism:

Nicotiana benthamiana; Pseudomonas syringae pv. syringae; Pseudomonas amygdali pv. tabaci

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32196 GPL27032 GPL32197

27 Samples

Download data: CSV, TXT

(Submitter supplied) 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. more...

Organism:

Pseudomonas syringae pv. actinidiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32919

2 Samples

Download data: BW, NARROWPEAK

(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) To analyze the antisense transcripts, we performed LM-seq for Pesudomonas aeruginosa ∆algR and Pesudomonas syringae ∆rhpS and their corresponding WT strain. Date-minging in ChIP-seq and HT-SELEX results from public dataset, we got the TF binding sites (TFBS) across genome. Coupling analysis with LM-seq and these TFBS, our results revealed that the coding region binding TFs regulate antisense RNA transcription by regulating the activity of cryptic promoters.

Organism:

Pseudomonas aeruginosa; Pseudomonas syringae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30212 GPL28819

8 Samples

Download data: BW

(Submitter supplied) Purpose: The outcome of host–pathogen interactions is thought to reflect the offensive and defensive capabilities of both players. When plants interact with Pseudomonas syringae, several well-characterized virulence factors contribute to early bacterial pathogenicity, including the type III secretion system (T3SS), which must be activated by signals from the plant and environment to allow the secretion of virulence effectors. more...

Organism:

Pseudomonas syringae pv. tomato str. DC3000; Pseudomonas sp.; Pseudomonas syringae pv. actinidiae str. CRAFRU8.43

Type:

Expression profiling by array

Platform:

GPL29584

36 Samples

Download data: TXT

(Submitter supplied) This RNA-seq dataset is from RNA sample collected using the physical seperation technique previously used in our lab (Lovelace 2018). The goal is to look at DC3000 AlgU regulon under pattern triggered immunity.

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24578

18 Samples

Download data: TXT

(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) This RNA-seq analysis examined the global effect of the RNA binding RsmA proteins in P. syringae under the T3SS-inducing condition and in KB medium. The results showed differential expression of more than 50% genes in the genome, which include significant down-regulation of T3SS genes.

Organism:

Pseudomonas syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29440

18 Samples

Download data: TXT

(Submitter supplied) Pseudomonas syringae was grown on minimal media and King's B medium. The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. The summer course was funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis".

Organism:

Pseudomonas syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29316

6 Samples

Download data: CSV

(Submitter supplied) Purpose: Pseudomonas syringae pv. actinidiae (Psa) is a phytopathogen that causes devastating bacterial canker in kiwifruit. Among five biovars defined by genetic, biochemical and virulence traits, Psa3 is the most aggressive and is responsible for the most recent reported outbreaks, but the molecular basis of its heightened virulence is unclear. A custom P. syringae multi-strain whole-genome microarray platform, encompassing biovars Psa1, Psa2 and Psa3 and the well-established model P. more...

Organism:

Pseudomonas syringae pv. actinidiae; Pseudomonas sp.; Pseudomonas syringae pv. tomato

Type:

Expression profiling by array

Platform:

GPL29584

60 Samples

Download data: TXT

(Submitter supplied) Blue light perception by epiphytic Pseudomonas syringae drives chemoreceptor expression enabling efficient plant infection

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by array

Platform:

GPL23823

16 Samples

Download data: TXT

(Submitter supplied) Many bacteria can transition from a planktonic lifestyle to life attached to a surface. Changes in gene expression have been documented in bacteria in mature biofilms, but few studies have looked at gene expression during the initial stages of surface attachment. To investigate this, we performed RNA-Seq using the model organism Pseudomonas syringae B728a which has been found in rivers and lakes but is known for living on the leaf surface. more...

Organism:

Pseudomonas syringae pv. syringae B728a

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29146

6 Samples

Download data: TXT