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| Status |
Public on Apr 20, 2020 |
| Title |
Widespread targeting of nascent transcripts by RsmA in Pseudomonas aeruginosa |
| Organism |
Pseudomonas aeruginosa PAO1 |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
In the opportunistic pathogen Pseudomonas aeruginosa RsmA is an RNA-binding protein that plays critical roles in the control of virulence, interbacterial interactions and biofilm formation. Although RsmA is thought to exert its regulatory effects by binding full-length transcripts, the extent to which RsmA binds nascent transcripts has not been addressed. Moreover, which transcripts are direct targets of this key post-transcriptional regulator is largely unknown. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing, with cells grown in the presence and absence of the RNA polymerase inhibitor rifampicin, we identify hundreds of nascent transcripts that RsmA associates with in P. aeruginosa. We also find that the RNA chaperone Hfq targets a subset of the RsmA-associated nascent transcripts and that the two RNA-binding proteins can exert regulatory effects on common targets. Our findings establish that RsmA associates with many transcripts as they are being synthesized in P. aeruginosa, identify the direct targets of RsmA, and suggest that RsmA and Hfq may act in a combinatorial fashion on certain target transcripts. More broadly, our data suggest that the binding of post-transcriptional regulators to nascent transcripts may be commonplace in bacteria where distinct regulators can function alone or in concert to achieve control over the translation of transcripts as soon as they emerge from RNA polymerase.
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| Overall design |
ChIP-seq: Genome-wide locations of RsmA (with and without rifampicin treatment) Hfq. Additionally, we assess the locations of RsmA in the absence of hfq and the locations of Hfq in the absence of rsmA & rsmF.
ChIP-seq: Please note that each bed file generated from all replicates is linked to the corresponding Sample*A records.
RNA-seq: RNA-sequencing of P. aerugionsa strain PAO1, PAO1 ∆rsmA ∆rsmF, and PAO ∆hfq
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| Contributor(s) |
Gebhardt MJ, Kambara TK, Ramsey KM, Dove SL |
| Citation(s) |
32332166 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 AI143771 |
Global post-transcriptional regulators in P. aeruginosa |
CHILDREN'S HOSPITAL |
SIMON L DOVE |
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| |
| Submission date |
Oct 02, 2019 |
| Last update date |
Jul 20, 2020 |
| Contact name |
Michael J Gebhardt |
| Organization name |
University of Iowa
|
| Department |
Department of Microbiology and Microbiology
|
| Lab |
Gebhardt
|
| Street address |
431 Newton Road, 200A EMRB
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platforms (2) |
| GPL18782 |
Illumina HiSeq 2500 (Pseudomonas aeruginosa PAO1) |
| GPL23999 |
Illumina NextSeq 500 (Pseudomonas aeruginosa PAO1) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA575528 |
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