GEO DataSets

(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, 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 bacterial Lon protease participates in a variety of biological processes. In Pseudomonas syringae, mutation of lon is known to activate hrpL and a few hrpL-regulated genes in the rich medium. The elevated expression of hrpL and hrpL-regulated genes results from of increased stability of HrpR, the transcriptional activator of hrpL, in the lon mutant. Here we conducted a microarray analysis to determine genes that are differently expressed in the lon- mutant of P. more...

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by array

Platform:

GPL3496

3 Samples

Download data: FTR, NDF, NGD, TIFF, 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) Although the ubiquitous bacterial secondary messenger cyclic diguanylate (c-di-GMP) plays important roles in various cellular functions including the formation of biofilm in a wide range of bacteria, its function in model plant pathogen Pseudomonas syringae is largely elusive. In order to test this in P. syringae, we overexpressed a diguanylate cyclase (YedQ) and a phosphodiesterase (YhjH) that are originally from Escherichia coli, resulting in high and low c-di-GMP levels in P. more...

Organism:

Pseudomonas syringae pv. syringae B728a

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25646

6 Samples

Download data: XLSX

(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) 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) PSPTO_2222 and PSPTO_2222-2223 deletions mutants were grown in MM or KB, and their expression profiles were analyzed.

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by array

Platform:

GPL3496

9 Samples

Download data: CALLS, FTR, PAIR, TIFF

(Submitter supplied) Lon protease is known to regulate various transcriptional regulators in other bacterial organisms. To understand whether lon protease is involved in transcriptional changes in Vibrio cholerae, wholel-genome level transcriptional profiling was performed using custom microarrays. Transcriptomes of lonA mutant and wild-type strains were compared in this study.

Organism:

Vibrio cholerae

Type:

Expression profiling by array

Platform:

GPL20916

6 Samples

Download data: GPR

(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) 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) 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) ProQ has become a paradigm for the emerging family of FinO domain-containing RNA binding proteins. ProQ in Salmonella enterica has been shown to act as a global RNA binding protein as it interacts with a plethora of sRNAs and mRNAs. However, little was known about processes ProQ regulates in Salmonella which have precluded to functionally characterize ProQ in vivo. In here, we show that ProQ represses the utilization of succinate as carbon source. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platforms:

GPL20056 GPL22775

24 Samples

Download data: WIG, XLSX

(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