GEO DataSets

(Submitter supplied) While nucleotide sequences determine an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, differences in methylation can be used to identify incoming DNA, for example from bacteriophages. Restriction enzymes detect the methylation status at specific sequence motifs, and cleave improperly methylated, foreign DNA. Furthermore, methylation of key genetic regions can influence gene expression and hence phenotype. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23128

4 Samples

Download data: TXT

(Submitter supplied) Burkholderia cepacia complex bacteria comprise opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. These microorganisms produce exopolysaccharides which are considered virulence determinants. Here, we report the isolation of an evolved nonmucoid variant (17616nmv) after the ancestor, Burkholderia multivorans ATCC 17616, was subjected to prolonged stationary phase. more...

Organism:

Burkholderia multivorans; Burkholderia cenocepacia J2315; Burkholderia multivorans ATCC 17616

Type:

Expression profiling by array

Platform:

GPL13356

6 Samples

Download data: CEL

(Submitter supplied) In this work, high-throughput RNA sequencing was used to assess transcriptomic alteration in Burkholderia cenocepacia K56-2 in the early stages of interaction with host-cell surface. Giant plasma membrane vesicles (GPMVs) from 16HBE14o- bronchial epithelial cell line were produced and used as a cell-like alternative. RNAseq was performed and the expression of the adherent (GPMV-attached) and non-adherent (planktonic control) bacteria were compared. more...

Organism:

Burkholderia cenocepacia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28995

6 Samples

Download data: TXT

(Submitter supplied) Purpose - To establish the response of B. cenocepacia K56-2 to growth in copper, and to characterise the BCAM0442/3 copper-sensing TCS. Methods - RNA-seq of the response WT and Δbcam0442/3 B. cenocepacia K56-2 to mid-log phase growth in LB with or without 1 mM CuCl2 was performed. Results - Characterisation of the overall response of B. cenocepacia K56-2 to copper, as well as establishing that BCAM0442/3 regulates the CopABCDE system in B. more...

Organism:

Burkholderia cenocepacia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29736

12 Samples

Download data: CSV

(Submitter supplied) Burkholderia multivorans comprises opportunistic bacteria infecting hosts such as cystic fibrosis (CF) patients. Bcc long-term infection of CF patient airways has been associated with emergence of phenotypic variation including the mucoid-to-nonmucoid colony morphotype. Here we studied three Burkholderia multivorans clonal isolates (mucoid D2095 (BM11L), and nonmucoid D2214G and D2214P) and a laboratory nonmucoid variant (BM11L-nmv1) obtained under prolonged stationary phase. more...

Organism:

Burkholderia multivorans; Burkholderia multivorans ATCC 17616; Burkholderia cenocepacia J2315

Type:

Expression profiling by array

Platform:

GPL13356

12 Samples

Download data: CEL

(Submitter supplied) Members of the diazeniumdiolate class of natural compounds show great potential for drug development. Yet, their biosynthesis has remained elusive to date. Here, we identify a gene cluster directing the biosynthesis of the diazeniumdiolate compound fragin in Burkholderia cenocepacia H111. We provide evidence that fragin is a metallophore and that metal chelation is the molecular basis of its antifungal activity. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23128

9 Samples

Download data: TXT

(Submitter supplied) In this study, we have analysed the transcriptional profile of B. cenocepacia H111 upon artificially altering the global cellular c-di-GMP levels. A total of 111 genes was found to be differentially expressed, of which 96 genes were down-regulated when c-di-GMP concentrations were increased. The BDSF, AHL and c-di-GMP regulons overlap for the regulation of 24 genes. Intriguingly, at a high intracellular c-di-GMP level expression of the AHL synthase cepI was found to be more than 10-fold down-regulated. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

8 Samples

Download data: TXT

(Submitter supplied) Burkholderia cenocepacia is a versatile opportunistic pathogen that survives in a wide variety of environments, which can be limited in nutrients such as nitrogen. We previously showed that B. cenocepacia sigma factor s54 played a major role in control of nitrogen assimilation and virulence. In this work, we investigated the role of the s54 enhancer binding protein NtrC in controlling the response to nitrogen limitation and virulence. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23128

6 Samples

Download data: TXT

(Submitter supplied) Within this work we identified and characterized gene Bmul_2557 (ldhR) of B. multivorans ATCC 17616, a bacterial species associated with chronic respiratory infections in cystic fibrosis patients. LdhR belongs to the LysR-type family of transcriptional regulators and its deletion from the B. multivorans genome affected considerably the formation of planktonic cellular aggregates and surface-attached biofilms.

Organism:

Burkholderia cenocepacia J2315; Burkholderia multivorans; Burkholderia multivorans ATCC 17616

Type:

Expression profiling by array

Platform:

GPL13356

9 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Burkholderia cenocepacia

Type:

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

Platform:

GPL19185

11 Samples

Download data

(Submitter supplied) BACKGROUND: We identified that a putative CzcRS-like two-component system (TCS) in Burkholderia cenocepacia K56-2 is required for heavy metal resistance and virulence. To investigate this TCS further, we applied RNA-seq to determine the transcriptional response of wildtype and CzcRS-deficient B. cenocepacia to subinhibitory concetrations of zinc. METHODS. Wildtype B. cenocepacia K56-2 was cultured in LB broth with and without 1.5 mM zinc chloride. more...

Organism:

Burkholderia cenocepacia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19185

9 Samples

Download data: TAB, TXT

(Submitter supplied) BACKGROUND: We identified that a putative CzcRS-like two-component system (TCS) in Burkholderia cenocepacia K56-2 is required for heavy metal resistance and virulence. In an attempt to identify genes directly regulated by the CzcR response regulator, we performed ChIP-seq analysis to identify genomic regions bound by CzcR. METHODS. Sequence encoding a FLAG octapeptide (Sigma-Aldrich) was introduced to the 3’ end of the czcR gene at its native chromosomal position in wild-type B. more...

Organism:

Burkholderia cenocepacia

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19185

2 Samples

Download data: TXT

(Submitter supplied) Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression level. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins and the two component regulatory system ntrBC, B. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

5 Samples

Download data: TXT

(Submitter supplied) Individual normalized intensity of Burkholderia cenocepacia and Burkholderia seminalis hybridized in a B. cenocepacia array

Organism:

Burkholderia cenocepacia; Burkholderia seminalis

Type:

Genome variation profiling by array

Platforms:

GPL18793 GPL18776

429 Samples

Download data: TXT

(Submitter supplied) In Burkholderia cenocepacia H111, the large surface protein BapA plays a crucial role in the formation of highly structured communities, known as biofilms. We have recently demonstrated that Quorum sensing (QS) is necessary for the maximal expression of bapA. In this study we identify a protein from the IclR family of transcriptional regulators that, in conjunction with QS, controls biofilm formation by affecting the expression of bapA. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

2 Samples

Download data: TXT

(Submitter supplied) Hfq proteins are RNA chaperones that play a critical role in post-transcription regulation of gene expression. Bacteria of the Burkholderia cepacia complex harbor two distinct and functional Hfq proteins, the Hfq and Hfq2. We have previously performed the functional analysis of Hfq and Hfq2 in the pathogen Burkholderia cenocepacia J2315. In order to examine the impacts of each RNA chaperone on the global transcriptome of B. more...

Organism:

Burkholderia cenocepacia J2315; Burkholderia cenocepacia; Burkholderia multivorans ATCC 17616

Type:

Expression profiling by array

Platform:

GPL13356

9 Samples

Download data: CEL, TXT

(Submitter supplied) B. cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis (CF). In the CF lung, bacteria grow to high densities within the viscous mucus that is limited in oxygen. Pseudomonas aeruginosa, the dominant pathogen in CF patients, is known to grow and survive under oxygen-limited to anaerobic conditions by using micro-oxic respiration, denitrification and fermentative pathways. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

2 Samples

Download data: TXT

(Submitter supplied) The bacterial tyrosine (BY) kinase family comprises the major group of bacterial enzymes endowed with tyrosine kinase activity. We have previously shown that the BceF protein from Burkholderia cepacia IST408 belongs to this BY kinase family and is involved in the biosynthesis of the exopolysaccharide cepacian. However, little is known about the extent of regulation in the cell by this kinase protein. more...

Organism:

Burkholderia multivorans ATCC 17616; Burkholderia cepacia; Burkholderia cenocepacia J2315

Type:

Expression profiling by array

Platform:

GPL15600

10 Samples

Download data: CEL

(Submitter supplied) Quorum sensing in Burkholderia cenocepacia H111 involves two signalling systems that depend on different signal molecules, namely N-acyl homoserine lactones (AHLs) and the diffusible signal factor cis-2-dodecenoic acid (BDSF). Previous studies have shown that AHLs and BDSF control similar phenotypic traits, including biofilm formation, proteolytic activity and pathogenicity. In this study we mapped the BDSF stimulon by RNA-Seq and shotgun proteomics analysis. more...

Organism:

Burkholderia cenocepacia H111

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16128

3 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Burkholderia multivorans; Burkholderia multivorans ATCC 17616; Burkholderia cenocepacia J2315

Type:

Expression profiling by array; Other

Platform:

GPL13356

10 Samples

Download data: CEL