GEO DataSets

(Submitter supplied) We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

12 Samples

Download data: GPR

(Submitter supplied) Microarray analysis was used to identify genes that were controlled by AmyR in minimal and on immature pear fruits. Consistent with amylovoran production, an inverse correlation was observed between amyR expression and the expression level of amylovoran biosynthetic genes in liquid media. Interestingly, over-expression of AmyR suppressed the expression of type III secretion system genes including hrpA, hrpN and dspEF after pear fruit infection. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

14 Samples

Download data: GPR

(Submitter supplied) RNA-seq analysis was performed to examine the sRNA transcripts in wild type E. amylovora 1189 and in the deletion mutant of hfq, at 6 and 12 hours of culture in hrp-inducing minimal medium.

Organism:

Erwinia amylovora

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18131

12 Samples

Download data: GTF, TXT

(Submitter supplied) Microarray analysis of E. amylovora treated with compounds no. 3 and no. 9 identified a total of 588 significantly differentially expressed genes. Among them, 95 and 78 genes were, respectively, induced and suppressed by both compounds as compared to DMSO control. Majority of T3SS genes in E. amylovora including hrpL and avrRpt2 effector gene were suppressed by both compounds. Compound no. 3 also suppressed the transcription of amylovoran precursor and biosynthesis genes. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

8 Samples

Download data: GPR

(Submitter supplied) This RNA-seq analysis mainly examined the global effect of stringent resonse in E. amylovora under the T3SS-inducing condition. The (p)ppGpp mutant showed differential expression of more than 30% genes in the genome, which include significant down-regulation of T3SS genes and gene related to motiliey. On the other hand, genes involved in amino acid biosynthesis, translation, SOS response, DNA replication, chromosome segregation, as well as nucleotide metabolism, fatty acid and lipid biosynthesis were significantly up-regulated in (p)ppGpp mutant. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26279

6 Samples

Download data: TXT

(Submitter supplied) This RNA-seq analysis examined the global effect of CsrA and its non-coding small RNA (ncsRNA) csrB in E. amylovora under the T3SS-inducing condition. The csrA mutant showed differential expression of more than 20% genes in the genome, which include significant down-regulation of T3SS genes and those required for cell growth and viability. On the other hand, the csrB mutant exhibited significant up-regulation of most major virulence genes, suggesting antagonistic effect of csrB on CsrA targets.

Organism:

Erwinia amylovora

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26279

9 Samples

Download data: TXT

(Submitter supplied) Xylella fastidiosa regulates traits important to both virulence of grape as well as colonization of sharpshooter vectors via its production of a fatty acid signal molecule known as DSF whose production is dependent on rpfF. While X. fastidiosa rpfF mutants exhibit increased virulence to plants they are unable to be spread from plant to plant by insect vectors. To gain more insight into the traits that contribute to these processes, a DNA microarray for this species was designed and utilized to determine the RpfF-dependent regulon by transcriptional profiling. more...

Organism:

Xylella fastidiosa 9a5c; Xylella fastidiosa Temecula1; Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL15652

1 Sample

Download data: TXT

(Submitter supplied) The Cj1223c gene was cloned downstream of a strong promoter into the replicating plasmid pRY108, and was highly expressed in the wild type Campylobacter jejuni 81-176 strain (overexpressed). The Cj1223c gene was knocked out by allelic replacement in the 81-176 strain background (mutant). This mutant also carried an empty pRY108 vector. The Cj1223c overexpressing strain and the mutant were grown overnight in liquid broth, supplemented with kanamycin. more...

Organism:

Campylobacter jejuni

Type:

Expression profiling by array

Platform:

GPL2782

8 Samples

Download data

(Submitter supplied) Quorum sensing (QS) in Xanthomonas axonopodis pv. citri, the causal agent of citrus canker, is mediated by a diffusible signal factor (DSF). QS is required for the full virulence of X. axonopodis pv. citri in planta. Mutations in rpfF, rpfC and rpfG, the core genes of QS, decreased the production of extracellular proteases and bacterial motility. Comparison of the transcriptomes of QS mutants with that of the wild type stain revealed that QS temporally regulates the expression of a large set of genes, including genes involved in chemotaxis and flagellar biosynthesis, genes related to metabolism, genes encoding virulence traits such as type II secretion system substates, type III secretion system and effectors. more...

Organism:

Xanthomonas citri pv. citri str. 306; Xanthomonas citri

Type:

Expression profiling by array

Platform:

GPL10890

6 Samples

Download data: TXT

(Submitter supplied) We have exploited a spontaneously isolated mutant IgaA(T191P) that is near-maximally activated for the Rcs system, to identify a vast set of genes that respond, and report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for growth of Salmonella in macrophages, although when highly activated, the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. more...

Organism:

Salmonella; Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica

Type:

Expression profiling by array

Platforms:

GPL1835 GPL4804 GPL3788

30 Samples

Download data

(Submitter supplied) The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen Staphylococcus aureus. We identified a highly conserved ten base pair palindromic sequence (5’ ACAAATTTGT 3’) located upstream from GraR-regulated genes (mprF and the dltA and vraFG operons), which we show to be essential for transcriptional regulation by GraR and induction in response to colistin, a bacterial CAMP, suggesting it is the likely GraR binding site. more...

Organism:

Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus

Type:

Expression profiling by genome tiling array

Platform:

GPL11308

6 Samples

Download data: PAIR

(Submitter supplied) In response to osmolarity, Salmonella enterica serotype Typhi (S. Typhi) regulates genes required for Vi capsular antigen expression oppositely to those required for motility and invasion. Previous studies suggest that osmoregulation of motility, invasion and capsule expression is mediated through the RcsC/RcsD/RcsB phosphorelay system. Here we performed gene expression profiling and functional studies to determine the role of TviA, an auxiliary protein of the RcsB response regulator, in controlling virulence gene expression in S. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhi; Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL8446

4 Samples

Download data: GPR

(Submitter supplied) Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium. We are primarily interested in gene regulation by three predicted LacI regulators. more...

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

36 Samples

Download data: TXT

(Submitter supplied) We performed chromatin immunoprecipitation on microarray (ChIP-chip) transcriptional profiling of the SsrB regulator of Salmonella enterica Typhimurium to better characterize its regulon and to identify the DNA-recognition element coordinating its specific interaction at cis-regulatory sites. SsrB, the response regulator of the two component regulatory system SsrA-SsrB encoded within the Salmonella Pathogenicity Island (SPI-2), directs transcriptional activation of the closely associated type three secretion system (T3SS) also encoded at this locus. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10008

4 Samples

Download data: TXT

(Submitter supplied) RcsB is a transcriptional regulator that controls expression of numerous genes in Enterobacteriaceae. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such a large number of genes, we performed structural and in vitro and in vivo functional studies with different RcsB variants. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27045

24 Samples

Download data: TSV

(Submitter supplied) Haemophilus ducreyi 35000HPcpxRpML125 which over-expresses CpxR in a CpxR deletion background, was compared to it vector alone counterpart (35000HPcpxRpLS88) in hopes to elucidate members of the CpxRA regulon.

Organism:

[Haemophilus] ducreyi; [Haemophilus] ducreyi 35000HP

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) Comparative analysis of the global gene expression of a Haemophilus ducreyi 35000HP cpxA deletion mutant relative to the wild type strain

Organism:

[Haemophilus] ducreyi; [Haemophilus] ducreyi 35000HP

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) Investigation of whole genome gene expression level changes in a B. suis 1330 regA mutant, compared to the wild-type strain. The two-component system RegBA of Brucella suis plays a central role in the control of respiratory systems adapted to oxygen deficiency. The mutant strain is affected in long-term persistence in vitro (this study) and in chronic infection in vivo (Abdou, E et al. 2013, Infect.Immun. more...

Organism:

Brucella suis; Brucella suis 1330

Type:

Expression profiling by array

Platform:

GPL22261

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA and phoB mutants when grown in phosphate-rich and phosphate-low medium

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL7345

16 Samples

Download data: TXT

(Submitter supplied) The two-component system qseBC is a putative prokaryotic adrenergic receptor. In Aggregatibacter actinomycetemcomitans (Aa), it was shown that the qseBC responds significantly to the presence of both catecholamines and ferrous iron. In addition, growth is significantly increased in the presence of both. Therefore, we performed a custom Aa microarray in order to determine the effects of catecholamines and catecholamines and iron (CAT-Fe) on Aa.

Organism:

Aggregatibacter actinomycetemcomitans

Type:

Expression profiling by array

Platform:

GPL20179

9 Samples

Download data: TXT