Gene expression profile of pellicle cells of Pseudomonas aeruginosa
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ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa
PROVIDER: GSE24784 | GEO | 2011/03/31
SECONDARY ACCESSION(S): PRJNA132233
REPOSITORIES: GEO
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Project description:To investigate the gene expression profile of pellicle cells of Pseudomonas aeruginosa, microarray analysis was performed. Transcriptome profiles of pellicle cells and planktonic cells grown in LB medium were determined by Affymetrix GeneChip. Gene expression pattern that is specific to pellicle cells was evaluated by comparing the data set with that of planktonic cells. Pseudomonas aeruginosa wild type (PAO1ut) strain was cultivated aerobically in LB in Erlenmeyer flasks under static or shaking conditions, and total RNAs were extracted at 24 hours (static culture) and early stationary phase (OD600 = 1.4, shaking culture). The experiment was performed in duplicate independent cultures.
2011-03-31 | E-GEOD-24784 | biostudies-arrayexpress
Project description:Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. In recent years, biofilm development of S. oneidensis has been extensively studied because it is essential to reduce solid metals. As a special form of biofilm, however, pellicles are largely overlooked. The goal of this work was to understand requirements of S. oneidensis pellicle formation and the molecular basis of pellicle formation. We demonstrated that successful pellicle formation and survival was likely to require the threshold level of cell density and higher concentration of oxygen. Proteinase K and EDTA were potent pellicle disrupter. DNA microarray experiments were used to study the gene expression profile of young air–liquid interface pellicle relative to planktonic cells, which indicated that the air–liquid interface pellicle was more metabolically active than the planktonic cells. Most notably, consistently up-regulation of iron or heme uptake and transportation proteins was observed in the S. oneidensis MR-1 pellicle. However, neither the hmuT nor hugA heme transport mutant was defective in pellicle formation. An examination of the influence of several metal cations on the anti-pellicle activity of EDTA showed that Ca (II), Mn(II), Cu(II), and Zn(II) fully protected S. oneidensis MR-1 pellicle against EDTA treatment while additional of iron enabled the initiation of pellicle formation but maturation was significantly impaired. Collectively, iron was less important than other metals with respect to pellicle formation in S. oneidensis. A fresh colony grown overnight on a LB plate was used to inoculate 50 ml LB and incubated in a shaker (200 rpm) to an OD600 of 0.8 at the room temperature. This culture was then diluted 500-fold with fresh LB, resulting in the starting cultures. Aliquots of 30ml starting cultures were transferred to 50-ml Pyrex beakers and allowed to develop pellicles at the room temperature. When a complete but thin (young pellicle) at the interface were formed (about 30h hours), planktonic culture and pellicle were separated and applied to centrifugation at 8000 rpm for 3 min at room temperature. 3 parallel starting cultures were used and 3 samlpes of pellicle cells or planktonic cells were collected at 30h. RNA from the pellicle cells was fluorescently labeled with Cy3, and that from the planktonic was labeled with Cy5.
2010-09-01 | E-GEOD-14331 | biostudies-arrayexpress
Project description:Biofilm formation by Pseudomonas aeruginosa relies on specific changes in gene expression. Some of these genes, for instance, control antibiotic resistance. We used microarrays to detail the global programme of gene expression underlying biofilm formation and identified distinct classes of up-regulated genes during this process. Pseudomonas aeruginosa PAO1 cells were grown as planktonic cells in LB broth for 4 hours (PC4) or 24 hours (PC24) and sessile cels for 24 hours.
2011-06-17 | E-GEOD-30021 | biostudies-arrayexpress
Project description:One of the most distinct features of Pseudoalteromonas sp. SCSIO 11900 is its ability to form a very robust pellicle than most Pseudoalteromonas strains. Thus we want to identify the genes essential for the pellicle formation of SCSIO 11900. We compared transcriptom profiles of planktonic cells, initial pellicle and mature pellicle of coral Pseudoalteromonas sp. SCSIO 11900 and revealed that some unique genes from horizontal gene transfer is involved in the pellicle formation of SCSIO 11900.
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Project description:Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C
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Project description:This SuperSeries is composed of the following subset Series:; GSE9989: Tobramycin Treatment of P. aeruginosa Biofilms Grown on CFBE41o- Cells; GSE9991: Tobramycin Treatment of Planktonic Pseudomonas aeruginosa Experiment Overall Design: Refer to individual Series
2008-06-18 | E-GEOD-10030 | biostudies-arrayexpress
Project description:To assess the role of two redox-sensitive transcriptional regulators, RoxSR and ANR, in Pseudomonas aeruginosa under aerobic conditions, microarray analysis was performed. Transcriptome profiles of roxSR mutant and anr mutant aerobically grown in LB medium were determined by Affymetrix GeneChip at both the exponential phase and early stationary phase and compared to that of the wild type strain.
2009-07-31 | GSE17296 | GEO
Project description:Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C.
2009-05-23 | E-GEOD-13871 | biostudies-arrayexpress
Project description:Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. In recent years, biofilm development of S. oneidensis has been extensively studied because it is essential to reduce solid metals. As a special form of biofilm, however, pellicles are largely overlooked. The goal of this work was to understand requirements of S. oneidensis pellicle formation and the molecular basis of pellicle formation. We demonstrated that successful pellicle formation and survival was likely to require the threshold level of cell density and higher concentration of oxygen. Proteinase K and EDTA were potent pellicle disrupter. DNA microarray experiments were used to study the gene expression profile of young air–liquid interface pellicle relative to planktonic cells, which indicated that the air–liquid interface pellicle was more metabolically active than the planktonic cells. Most notably, consistently up-regulation of iron or heme uptake and transportation proteins was observed in the S. oneidensis MR-1 pellicle. However, neither the hmuT nor hugA heme transport mutant was defective in pellicle formation. An examination of the influence of several metal cations on the anti-pellicle activity of EDTA showed that Ca (II), Mn(II), Cu(II), and Zn(II) fully protected S. oneidensis MR-1 pellicle against EDTA treatment while additional of iron enabled the initiation of pellicle formation but maturation was significantly impaired. Collectively, iron was less important than other metals with respect to pellicle formation in S. oneidensis.
2010-09-01 | GSE14331 | GEO
Project description:An antivirulence approach targets bacterial virulence rather than cell viability in the antibiotic approach that can readily lead to drug resistance. Opportunistic human pathogen Pseudomonas aeruginosa produces a variety of virulence factors, and biofilm cells of this bacterium are much more resistant to antibiotics than planktonic cells. To identify novel inorganic antivirulence compounds, the dual screenings of thirty-six metal ions were performed to identify that zinc ions and ZnO nanoparticle inhibited the pyocyanin production and biofilm formation in P. aeruginosa without affecting the growth of planktonic cells. Moreover, zinc ion and ZnO nanoparticle markedly reduced the production of 2-heptyl-3-hydroxy-4(1H)-quinolone and siderophore pyochelin, while increased the production of another sideropore pyoverdine and swarming motility. Further, zinc ion and ZnO nanoparticle clearly suppressed hemolytic activity in P. aeruginosa. Transcriptome analyses showed that ZnO nanoparticle induced zinc cation efflux pump czc operon, porin genes (oprD and opdT), and Pseudomonas type III repressor A ptrA, while repressed pyocyanin-related phz operon, which partially explains the phenotypic changes. Overall, ZnO nanoparticle is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection. P. aeruginosa Genechip Genome Array (Affymetrix, P/N 900339) was used in order to study the cells after the addition of ZnO nanoparticles. DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).
2015-05-25 | E-GEOD-46947 | biostudies-arrayexpress