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Fraction-wise RNA-seq of the Salmonella Typhimurium SL1344 cell lysate resolved on a 10-40% glycerol gradient

ABSTRACT: While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset is a representative experiment carried out to characterize sedimentation properties of bacterial transcripts genome-wide. Downstream analysis of their sedimentation profiles enables their biochemical classification and is a prerequisite for identification of global RNA-binding proteins.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium

PROVIDER: GSE62986 | GEO | 2016/08/29

SECONDARY ACCESSION(S): PRJNA266347

REPOSITORIES: GEO

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RIP-seq of RNA associated in vivo with the ProQ, Hfq or CsrA proteins, performed in Salmonella Typhimurium SL1344 or Escherichia coli W3110

Project description:While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset includes representative RIP experiments carried out to characterize the in vivo interactome of the bacterial global RNA-binding protein ProQ. They include a series of RIPs performed on a Salmonella Typhimurium SL1344 ProQ-3xFLAG strain grown to the exponential (OD600=0.5), transition (OD600=2.0) or stationary (6 hours after cells reached OD600=2.0) phases; a RIP perfomed on an Escherichia coli W3110 ProQ-3xFLAG strain grown to the transition phase; a control series of RIPs performed on Salmonella Typhimurium SL1344 ProQ-3xFLAG and PhoP-3xFLAG strains grown to the transition phase. The first series shows how the ProQ RNA interactome evolves over growth in Salmonella, the second reveals ProQ targets in Escherichia, the third illustrates the lack of RNA-binding activity in a negative control, DNA-binding transcription regulator PhoP.

2016-08-29 | GSE62987 | GEO

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Project description:RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element for building a comprehensive catalogue of microbial RBPs.

2020-07-16 | PXD018422 | Pride

Role of ProQ in Salmonella virulence - in vitro

Project description:FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. Comparison with Hfq, Salmonella’s other major RNA chaperone, reinforces the notion that these two global RNA binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs, we show that STnc540 represses a virulence-related magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella infection and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.

2018-11-28 | GSE117255 | GEO

Role of ProQ in Salmonella virulence - pulse expression

2018-11-28 | GSE117252 | GEO

Role of ProQ in Salmonella virulence - dual RNA-Seq

2018-11-28 | GSE117236 | GEO

Biochemical partitioning of RNA collectives reveals ProQ as a global RNA chaperone in bacteria

Project description:The vast number of noncoding RNAs in bacteria suggests that major post-transcriptional circuits beyond those controlled by the global RNA-binding proteins Hfq and CsrA may exist. To identify additional globally acting RNPs we have developed a method (gradient profiling by sequencing; Grad-seq) to partition the full ensemble of cellular RNAs based on their biochemical behavior. Consequently, we discovered transcripts that commonly interact with the osmoregulatory protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant RNA-binding protein with a wide range of targets, including a new class of ProQ-associated small RNAs that are highly structured and function to regulate mRNAs in trans. Based on its ability to chart the functional landscape of all cellular transcripts irrespective of their length and sequence diversity, Grad-seq promises to aid the discovery of major functional RNA classes and RNA-binding proteins in many organisms.

2017-07-21 | PXD003360 | Pride

Deep mutational scanning of RNA-binding protein ProQ suggests a mechanism of quality control by protease Lon

Project description:ProQ has become a paradigm for the emerging family of FinO domain-containing RNA binding proteins. ProQ in Salmonella enterica has been shown to act as a global RNA binding protein as it interacts with a plethora of sRNAs and mRNAs. However, little was known about processes ProQ regulates in Salmonella which have precluded to functionally characterize ProQ in vivo. In here, we show that ProQ represses the utilization of succinate as carbon source. The latter allowed applying deep mutational scanning to ProQ to identify residues within the protein important to its function in vivo. ProQ carries a FinO domain, responsible for RNA binding, as its N-terminal domain fused via a linker to a C-terminal domain with unknown function. Remarkably, residues within both the N-terminal domain and C-terminal domain of the protein are found to be essential for ProQ function. Mutations in the C-terminal lead to non-fuctional variants to regulate succinate utilization but capable to interact with RNA. On the contrary, mutations on the N-terminal domain leave ProQ functionally inactive to regulate ProQ function in vivo and to interact with RNA. Notably, the inability to interact with RNA render ProQ unstable. The latter leads to an active Lon protease mediated degradation suggesting that interaction with RNA represents a control mechanism to modulate ProQ turnover.

2021-11-24 | GSE174509 | GEO

RNA-RNA interactomes of Hfq and ProQ reveal overlapping and competing roles for RNA chaperones

Project description:In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is facilitated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To compare the contributions of Hfq and the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq, which allows global identification of two RNAs bound to the same protein. We detected hundreds of RNA pairs on ProQ. Intriguingly, 33% of the ProQ-bound RNA pairs are also found associated with Hfq, suggesting overlapping, complementary or competing roles for the two proteins.

2019-12-08 | GSE131520 | GEO

CLIP-seq of Salmonella ProQ in intracellular-like conditions

Project description:The aim of the project is to identify transcriptome-wide binding sites for the global RNA-binding protein ProQ in Salmonella during intracellular-like conditions.

2024-02-13 | GSE250014 | GEO

The role of the RNA chaperone protein ProQ in Pasteurella multocida

Project description:The Gram-negative pathogen Pasteurella multocida is responsible for many important animal diseases. While a number of P. multocida virulence factors have been identified, very little is known about how gene expression and protein production is regulated in this organism. One mechanism by which bacteria regulate transcript abundance and protein production is riboregulation, which involves the interaction of a small RNA (sRNA) with a target mRNA to alter transcript stability and/or translational efficiency. This interaction often requires stabilization by a ribosome binding protein such as ProQ or Hfq. In E. coli and other species, ProQ has been shown to play a critical role in stabilizing sRNA-mRNA interactions and preferentially binds to 3’ stem-loop regions of the mRNA transcripts, characteristic of intrinsic transcriptional terminators. The aim of this study was to determine the role of ProQ riboregulation in P. multocida and identify the RNA regions to which it binds. We assessed differentially expressed transcripts in a proQ mutant and identified sites of direct ProQ-RNA interaction using in vivo UV-crosslinking and analysis of cDNA (CRAC). These analyses demonstrated that ProQ binds to, and stabilises, ProQ-dependant sRNAs and transfer RNAs in P. multocida via adenosine enriched, highly structured sequences. The binding of ProQ to two RNA molecules was characterised and showed that ProQ bound within the coding sequence of the uncharacterized PmVP161_1121 and within the 3’ region of the sRNA Prrc13.

2022-03-02 | GSE196834 | GEO

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