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Series GSE233207

Query DataSets for GSE233207

Status

Public on Aug 21, 2023

Title

Use of transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates

Organisms

Pseudomonas aeruginosa; Pseudomonas aeruginosa UCBPP-PA14; Pseudomonas aeruginosa PAO1

Experiment type

Expression profiling by high throughput sequencing

Summary

In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts non-overlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding diguanylate cyclases. We demonstrate that the selection of sub-groups of clinical isolates with high versus low expression of regulatory genes served the identification of their downstream regulons. Thus, analyzing transcriptional profiles of clinical isolates with variant expression of diguanylate cyclase genes might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates, we were unable to confirm diguanylate specific gene regulation. It is possible that the elevated c-di-GMP concentrations observed in the clinical P. aeruginosa isolates were due to a memory response, in which the bacteria maintain a certain level of c-di-GMP even after being removed from the conditions that induced the production of c-di-GMP. Further studies would be needed to determine the specific mechanisms underlying this memory response in P. aeruginosa.

Overall design

RNASeq of different Pseudomonas aeruginosa PA14/PAO1 and clinical isolates with a mutation in PA14_03790 or PA14_23130 - planctonic growth in LB medium.

Contributor(s)

Gür M, Erdmann J, Will A, Häußler S

Citation(s)

Submission date

May 23, 2023

Last update date

Aug 21, 2023

Contact name

Matthias Preusse

E-mail(s)

matthias.preusse@helmholtz-hzi.de

Organization name

Helmholtz Center for Infection Research

Department

Molecular Bacteriology

Street address

Inhoffenstr. 7

City

Braunschweig

ZIP/Postal code

38124

Country

Germany

Platforms (3)

GPL26913	Illumina NovaSeq 6000 (Pseudomonas aeruginosa)
GPL27892	Illumina NovaSeq 6000 (Pseudomonas aeruginosa UCBPP-PA14)
GPL28916	Illumina NovaSeq 6000 (Pseudomonas aeruginosa PAO1)

Samples (24)

More...

GSM7412766	RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 at OD 2 replicate 1
GSM7412767	RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 at OD 2 replicate 2
GSM7412768	RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_23130 mutant at OD 2 replicate 1

GSM7412769	RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_23130 mutant at OD 2 replicate 2
GSM7412770	RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_03790 mutant at OD 2 replicate 1
GSM7412771	RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 ΔPA14_03790 mutant at OD 2 replicate 2
GSM7412772	RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 at OD 2 replicate 1
GSM7412773	RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 at OD 2 replicate 2
GSM7412774	RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA3177 mutant at OD 2 replicate 1
GSM7412775	RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA3177 mutant at OD 2 replicate 2
GSM7412776	RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA0290 mutant at OD 2 replicate 1
GSM7412777	RNASeq of planctonic culture of Pseudomonas aeruginosa PAO1 ΔPA0290 mutant at OD 2 replicate 2
GSM7412778	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 at OD 2 replicate 1
GSM7412779	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 at OD 2 replicate 2
GSM7412780	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA3177 mutant at OD 2 replicate 1
GSM7412781	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA3177 mutant at OD 2 replicate 2
GSM7412782	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA0290 mutant at OD 2 replicate 1
GSM7412783	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA0290 mutant at OD 2 replicate 2
GSM7412784	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 1
GSM7412785	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 2
GSM7412786	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 3
GSM7412787	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 4
GSM7412788	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 passage 18 at OD 2 replicate 1
GSM7412789	RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 passage 18 at OD 2 replicate 2

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE233207_reads_per_gene.csv.gz	255.3 Kb	(ftp)(http)	CSV
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record

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