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Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without iron.

ABSTRACT: The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response. Four biological replicates, independent RNA preparations, one dye swap.

ORGANISM(S): Agrobacterium tumefaciens

SUBMITTER: Jason Heindl

PROVIDER: E-GEOD-71138 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without iron.

Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response.

2015-07-22 | GSE71138 | GEO

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without manganese

Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response. Four biological replicates, independent RNA preparations, two dye swaps.

2015-07-24 | E-GEOD-71266 | biostudies-arrayexpress

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without manganese

Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response.

2015-07-24 | GSE71266 | GEO

Increased mutability of staphylococci in biofilms as a consequence of oxidative stress

Project description:In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies increased mutability in the biofilm. Transcriptional profiling revealed upregulation of the superoxide dismutase gene, sodA, in early biofilm cultures, also suggesting enhanced oxidative stress in these cultures. However, loss of the genes encoding superoxide dismutases or peroxidases did not specifically exacerabate biofilm mutability. In S. aureus SH1000, hydrogen peroxide was found to contribute to biofilm mutability. Three growth conditions (18 hr planktonic growth, 48 hr biofilm growth and 144 biofilm growth) of which there are three biological replicates of each

2012-03-01 | E-GEOD-35837 | biostudies-arrayexpress

Understanding environmental and biocide survival of Candida auris through transcriptional profiling

Project description:Candida auris is an enigmatic fungal pathogen, recently elevated to the Critical Priority group of fungal pathogens by the World Health Organisation. Of key concern is its ability to cause outbreaks within intensive and chronic care units, which is facilitated through biofilm formation. We investigated the susceptibility of phenotypically-diverse C. auris isolates to sodium hypochlorite (NaOCl) disinfection, and the subsequent role of biofilms in surviving disinfection using a dry-surface biofilm (DSB) model and transcriptomic profiling. Planktonic cells were tested for susceptibility to NaOCl using minimum inhibitory concentration and disinfection protocols. Biofilm formation using the DSB model consisted of consecutive 48 hr cycles with/without media across a 12-day period, assessed using viable counts, biomass assays, and microscopy. Disinfection efficacy was assessed using clinically relevant protocols of 500-1000 ppm for 1-5 min. RNA-sequencing was performed on untreated DSBs in comparison to planktonic cells. Isolates were found to be sensitive to NaOCl planktonically at concentrations ≤62.5 ppm, and grew robust biofilms using the DSB protocol. Biofilms developed tolerance to all NaOCl treatment parameters, with 2-4 log10-reductions in viable cells observed at highest concentrations. Transcriptomics identified ABC transporters and iron acquisition pathways as strongly upregulated in DSBs relative to planktonic cells. We have optimised a DSB protocol in which C. auris biofilms can mediate tolerance to adverse conditions such as NaOCl disinfection, suggesting a lifestyle through which this problematic yeast can environmentally persist and transmit. Mechanistically, the upregulation of small-molecule and iron transport pathways have been identified as potential facilitators of survival.

2023-08-07 | GSE239851 | GEO

Escherichia coli biofilms vs planktonic culture

Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol. Two condition experiments: E. coli biofilm vs E. coli planktonic cultures. Two biological replicates with independently grown and harvested biofilms or planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.

2013-12-30 | E-GEOD-24914 | biostudies-arrayexpress

Gene expression of E. coli MG1655 at attachment, colony formation and maturation during biofilm formation

Project description:Gene expression changes during biofilm formation processes were investigated. The gene expression was compared at attachment, colony formation and maturation during biofilm formation. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression pattern at attachment and colony formation processes showed similar pattern with those in planktonic exponential phase, and the gene expression pattern at maturation process showed similar pattern with those in planktonic stationary phase. During the maturation process, metabolic activities of the cells in the biofilms decreased, and the genes involved in the anaerobic respiration and efflux pumps were induced. The analysis revealed that gene expression pattern was changed and the physiological states were changed dramatically during maturation process in the biofilms. Keywords: time course Affymetrix E. coli antisense genome array was used to compare the gene expression among biofilm formation processes (attachment, colony formation and maturation) and planktonic cells (exponential phase and stationary phase). All samples were grown in MOPS minimal media with 0.2% glucose at 37ºC. Biofilms were grown on glass surface in flow cells (1 x 4 x 40 mm), and samples were taken at 2 h, 24 h and 72 h. Planktonic cell were grown for 6 h (exponential phase) and 24 h (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 5 different samples.

2009-04-01 | E-GEOD-13418 | biostudies-arrayexpress

Gene expression of E. coli MG1655 at attachment, colony formation and maturation during biofilm formation

2009-04-01 | GSE13418 | GEO

Differential gene expression between Salmonella Typhimurium biofilms on glass vs cholesterol surfaces

Project description:Salmonella spp. biofilms have been implicated in persistence in the environment and plant surfaces. In addition, Salmonella is able to form biofilms on the surface on cholesterol gallstones. The ability of Salmonella spp. on these surfaces is superior to biofilm formation on surfaces on glass or plastic. Thus, we hypothesized that Salmonella gene expression is specific during biofilm development on cholesterol surfaces. Flow through assays were performed whereby S. Typhimurium was inoculated into chambers coated with glass or cholesterol. At 24h post-inoculation, planktonic (from the flow through), biofilms (from glass or cholesterol) were collected. Thus we had 4 samples: Planktonic (2) and Biofilms (2), each with 2 biological replicates

2013-07-09 | E-GEOD-48604 | biostudies-arrayexpress

Pseudomonas aeruginosa Heme Metabolites Biliverdin IX and IX are Integral to Lifestyle Adaptations Associated with Chronic Infection

Project description:Pseudomonas aeruginosa is a versatile opportunistic pathogen requiring iron for its survival and virulence within the host. The ability to switch to heme as an iron source provides an advantage in chronic infection. We have recently shown the extracellular heme metabolites biliverdin IX (BVIX) and/or BVIX positively regulate the heme dependent cell surface signaling cascade. We further investigated the role of BVIX and BVIX in cell signaling utilizing allelic strains lacking a functional HemO (hemOin), or one reengineered to produce BVIX (hemO). Compared to PAO1 both strains show a heme dependent growth defect, decreased swarming and twitching and less robust biofilm formation. Interestingly, the motility and biofilm defects were partially rescued on addition of exogenous BVIX and BVIX. Utilizing LC-MS/MS we performed a comparative proteomics and metabolomics analysis of PAO1 versus the allelic strains in shaking and static conditions. In shaking conditions, the hemO allelic strains showed a significant increase in proteins involved in quorum sensing (QS), phenazine production and chemotaxis.Metabolite profiling further revealed increased levels of PQS and phenazine metabolites. In static conditions we observed a significant repression of chemosensory pathways and Type IV pili (TFP) biogenesis proteins as well as several phosphodiesterases associated with biofilm dispersal. We propose BVIX metabolites function as signaling and chemotactic molecules integrating heme utilization as an iron source into the adaptation of P. aeruginosa from a planktonic to sessile lifestyle.

2024-01-19 | PXD045835 | Pride

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