Show simple item record

dc.contributor.authorGerovac, Milan
dc.contributor.authorWicke, Laura
dc.contributor.authorChihara, Kotaro
dc.contributor.authorSchneider, Cornelius
dc.contributor.authorLavigne, Rob
dc.contributor.authorVogel, Jörg
dc.date.accessioned2021-02-26T15:54:05Z
dc.date.available2021-02-26T15:54:05Z
dc.date.issued2021-02-09
dc.identifier.citationmBio. 2021 Feb 9;12(1):e03454-20. doi: 10.1128/mBio.03454-20.en_US
dc.identifier.pmid33563827
dc.identifier.doi10.1128/mBio.03454-20
dc.identifier.urihttp://hdl.handle.net/10033/622757
dc.description.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.IMPORTANCE Stable complexes by cellular proteins and RNA molecules lie at the heart of gene regulation and physiology in any bacterium of interest. It is therefore crucial to globally determine these complexes in order to identify and characterize new molecular players and regulation mechanisms. Pseudomonads harbor some of the largest genomes known in bacteria, encoding ∼5,500 different proteins. Here, we provide a first glimpse on which proteins and cellular transcripts form stable complexes in the human pathogen Pseudomonas aeruginosa We additionally performed this analysis with bacteria subjected to the important and frequently encountered biological stress of a bacteriophage infection. We identified several molecules with established roles in a variety of cellular pathways, which were affected by the phage and can now be explored for their role during phage infection. Most importantly, we observed strong colocalization of phage transcripts and host ribosomes, indicating the existence of specialized translation mechanisms during phage infection. All data are publicly available in an interactive and easy to use browser.en_US
dc.language.isoenen_US
dc.publisherAmerican Society for Microbiology (ASM)en_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectGrad-seqen_US
dc.subjectPseudomonasen_US
dc.subjectPseudomonas aeruginosaen_US
dc.subjectRNA-binding proteinsen_US
dc.subjectbacteriophageen_US
dc.subjectinfectionen_US
dc.subjectnoncoding RNAen_US
dc.subjectphageen_US
dc.subjectΦKZen_US
dc.titleA Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions.en_US
dc.typeArticleen_US
dc.identifier.eissn2150-7511
dc.contributor.departmentHIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.en_US
dc.identifier.journalmBioen_US
dc.source.volume12
dc.source.issue1
refterms.dateFOA2021-02-26T15:54:06Z
dc.source.journaltitlemBio
dc.source.countryUnited States


Files in this item

Thumbnail
Name:
Gerovac et al.pdf
Size:
5.666Mb
Format:
PDF
Description:
Open Access publication

This item appears in the following Collection(s)

Show simple item record

Attribution 4.0 International
Except where otherwise noted, this item's license is described as Attribution 4.0 International