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| Status |
Public on May 04, 2022 |
| Title |
Global mapping of RNA-binding domains in multi-drug resistant Staphylococcus aureus |
| Organism |
Staphylococcus aureus subsp. aureus USA300 |
| Experiment type |
Other
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| Summary |
Using improved and robust biochemical methods, we present the first global analysis of RNA-binding proteins (RBPs) and RNA-binding domains (RBDs) in clinically relevant and multi-drug resistant Gram-positive bacteria. To validate our results in silico, we developed novel bioinformatics tools that compare RBDome data with ligand-binding site predictions generated by five different algorithms on a large number of S. aureus crystal structures. This revealed that the putative RBDs are highly enriched for predicted RNA-binding sites and basic and aliphatic amino acids, demonstrating the robustness of our approach. Surprisingly, we found that HTH-type DNA-binding and NAD and P-loop type Rossmann-fold proteins may also play a prominent role in post-transcriptional regulation in Gram-positive bacteria and we identified a common mode of RNA recognition for these domains. Subsequent in vivo validation studies showed that the HTH-type transcription factor CcpA, a master regulator of carbon metabolism in Gram-positive bacteria, is also a global post-transcriptional regulator and binds its RNA substrates at very specific distances from transcription terminators. Our novel experimental and computations tools are widely applicable, and our work provides an extremely valuable resource for groups studying post-transcriptional regulation and RNA-binding proteins in bacteria.
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| Overall design |
Two biological replicates of CRAC experiments with three experimental replicates each. CRAC experiments were performed with the parental USA300 strain and the strain expressing CcpA-HTF (HIS6-TEV-3xFLAG)
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| Contributor(s) |
Granneman S, Rei PA, Chu L |
| Citation(s) |
35610211 |
| |
| Submission date |
Dec 22, 2020 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Sander Granneman |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Edinburgh
|
| Department |
Centre for Synthetic and Systems Biology
|
| Lab |
Granneman lab
|
| Street address |
Mayfield Road, Kings Buildings, Waddington building, room 3.06
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JD |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL29525 |
Illumina NovaSeq 6000 (Staphylococcus aureus subsp. aureus USA300) |
| GPL29526 |
Illumina MiniSeq (Staphylococcus aureus subsp. aureus USA300) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA687253 |
| SRA |
SRP298955 |
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