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| Status |
Public on Jun 16, 2019 |
| Title |
A Cystic Fibrosis Pseudomonas aeruginosa Isolate Specialised to Catabolise Nucleic Acids |
| Organism |
Pseudomonas aeruginosa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We provide an insight to the DNA auxotrophy of P. aeruginosa PASS4 isolate. Better understanding of P. aeruginosa adaptations in the CF lung environment can have a great impact in the development of specialised treatment regimes aimed at the eradications of P. aeruginosa infections.
Methods: P. aeruginosa strains PAO1 and PASS4 were grown in minimal medium with either L-Asparagine or DNA as a carbon source, in biological triplicates. RNA was extracted and sequenced on Illumina HiSeq 1000 platform. The sequence reads that passed quality filters were analyzed using EdgePro and DESeq packages, as well as the Rockhopper tool.
Results: We mapped > 10 million paired sequence reads per sample to the genome of P. aeruginosa PAO1 and identified a total of 576 genes differentially expressed by PASS4 when grown in DNA (P value < 0.01, log2 fold-change 1< to < -1), with 322 genes upregulated and 254 genes downregulated. There were a total of 423 genes differentially expressed by PAO1 when grown in DNA (P value < 0.01, log2 fold-change 1< to <-1), with 359 genes upregulated and 64 genes downregulated . A total of 129 transcripts displayed similar expression patterns in both organisms, with 112 being upregulated and 17 down-regulated.
Conclusions: Our study identified that P. aeruginosa PASS4 was a purine auxotroph. Purine auxotropy may represent a viable microbial strategy for adaptation to DNA rich environments such as the CF lung.
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| Overall design |
mRNA profiles of P. aeruginosa strains PAO1 and PASS4 grown in minimal media with either DNA or L-Asparagine as a sole carbon source were generated by paired end sequencing, in triplicate, using Illumina HiSeq.
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| Contributor(s) |
Penesyan A, Kumar SS |
| Citation(s) |
31214142 |
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| Submission date |
Jun 21, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Anahit Penesyan |
| Organization name |
Mcquarie University
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| Street address |
E8A, Eastern road
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| City |
Macquarie University |
| State/province |
NSW |
| ZIP/Postal code |
2109 |
| Country |
Australia |
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| Platforms (1) |
| GPL18644 |
Illumina HiSeq 2000 (Pseudomonas aeruginosa) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA391260 |
| SRA |
SRP109989 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100287_PASS4_denovo_transcripts.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE100287_RAW.tar |
1.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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