Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces
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ABSTRACT:
PROVIDER: PRJNA802234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17869103_1.fastq.gz | Fastqsanger.gz | |||
| SRR17869103_2.fastq.gz | Fastqsanger.gz | |||
| SRR17869104_1.fastq.gz | Fastqsanger.gz | |||
| SRR17869104_2.fastq.gz | Fastqsanger.gz | |||
| SRR17869105_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces. Methods: Coupons of silicone, glass, and polycarbonate plastic were purchased from Biosurfaces Technologies (Catalog numbers: RD128-Si, RD128-GL, RD128-PC). Coupons were placed into a 24-well plate and conditioned in LB for at least 10 min prior to bacterial addition. LB was removed and replaced with 2mL of logarithmic phase bacterial culture in LB (OD600 0.7). At the indicated time point, the coupon was rinsed twice in PBS and placed into 1 mL of Trizol. Trizol was collected and stored at -80°C for RNA isolation. HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads. Reads were aligned to the reference PAO1 genome using Rockhopper. Results: A total of 833 genes were differentially expressed across the three surfaces. Most genes were reduced (522 genes) rather than elevated (269 genes), with 42 genes showing both elevated and reduced RNA levels across two or more surfaces. Conclusion: Bacteria had a nearly unique transcriptional response on each surface, with the vast majority regulated on only one surface
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Project description:Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. In fact, Shewanella species have been demonstrated to adhere to various surfaces and form biofilms. Global transcriptome profiling was performed on cells in the transition to surface-associated growth using different surfaces and conditions to understand molecular mechanisms underlying the initiation of microbe-surface interactions and the switch from planktonic to sessile life style.
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Project description:Pseudomonas aeruginosa is a pathogenic micro-organism responsible for many hospital-acquired infections. It is able to adhere to solid surfaces and develop an immobilised community or so-called biofilm. Many studies have been focusing on the use of specific materials to prevent the formation of these biofilms, but the reactivity of the bacteria in contact to surfaces remains unknown. In order to evaluate the impact of different materials on the physiology of Pseudomonas aeruginosa during the first stage of biofilm formation, i.e. adhesion, we investigated the total proteome of cells adhering to three materials: stainless steel, glass and polystyrene. Using tandem mass spectrometry performed at the PAPPSO proteomic platform, 930 proteins were identified, 70 of which were differentially expressed between the materials. Dysregulated proteins belonged to 19 PseudoCAP (Pseudomonas Community Annotation Project) functional classes, with a particular abundance of proteins involved in small molecule transport and membrane proteins. Notably, ten porins or porin precursors were under-produced in bacteria adhering to stainless steel when compared to those adhering to polystyrene and glass. Although adhesion to solid surfaces is an extracellular phenomenon, it involves not only extracellular proteins but also intracellular reactions, as observed with the dysregulation of 11 proteins involved in various metabolisms and five in protein translation. Overall, this work showed that during bacterial adhesion, P. aeruginosa senses the materials concerned and is able to modulate its physiology accordingly.
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Project description:We demonstrate that the versatile environmental bacterium Pseudomonas aeruginosa adapts a virulence phenotype after serial passage in Galleria mellonella as an invertebrate model host. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under non-inducing rich medium conditions. Transcriptional reprogramming seemed to be induced by a host-specific food source as reprogramming was also observed upon cultivation of P. aeruginosa in medium supplemented with polyunsaturated long-chain fatty acids. Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from LB-cultures grown to an OD600 =2. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings.
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Project description:DNA microarray analysis was employed to investigate the transcriptome response to nitric oxide in Pseudomonas aeruginosa. We focused on the role played by the nitric oxide-response regulators DNR and FhpR and an oxygen-response regulator ANR in the response. The transcriptome profiles of the P. aeruginosa strains before and after exposure to nitric oxide under the microaerobic conditions were analyzed. Wild type, its anr, dnr, and fhpR mutants, and the anr mutant that express dnr were used for the analyses.
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