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A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions.
| Content Provider | Europe PMC |
|---|---|
| Author | Gerovac, Milan Wicke, Laura Chihara, Kotaro Schneider, Cornelius Lavigne, Rob Vogel, Jörg |
| Editor | Ruby, Edward G. |
| Copyright Year | 2021 |
| Abstract | ABSTRACTThe Gram-negative rod-shaped bacterium Pseudomonas aeruginosa is not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and posttranscriptional regulation through the RNA-binding proteins Hfq, RsmA, and RsmN have been studied in detail, global information about stable RNA-protein complexes in this human pathogen is currently lacking. Here, we implement gradient profiling by sequencing (Grad-seq) in exponentially growing P. aeruginosa cells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs of P. aeruginosa, including 6S RNA with RNA polymerase and associated product RNAs (pRNAs). We observe specific clusters of noncoding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint that P. aeruginosa expresses a ProQ-like FinO domain-containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased cosedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded noncoding RNAs. Taken together, the Pseudomonas protein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell. |
| Page Count | 26 |
| Journal | Mbio |
| Volume Number | 12 |
| PubMed Central reference number | PMC8545117 |
| Issue Number | 1 |
| PubMed reference number | 33563827 |
| e-ISSN | 21507511 |
| DOI | 10.1128/mbio.03454-20 |
| Language | English |
| Publisher | American Society for Microbiology |
| Publisher Date | 2021-02-09 |
| Publisher Place | 1752 N St., N.W., Washington, DC |
| Access Restriction | Open |
| Rights License | This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Copyright © 2021 Gerovac et al. |
| Subject Keyword | Grad-seq Pseudomonas ΦKZ bacteriophage infection Pseudomonas aeruginosa RNA-binding proteins noncoding RNA phage |
| Content Type | Text |
| Resource Type | Article |
| Subject | Microbiology Virology |
