CsrA enters Hfq's territory: Regulation of a base‐pairing small RNA

Stenum, Thomas Søndergaard; Holmqvist, Erik

doi:10.1111/mmi.14785

Cited by 9 publications

(5 citation statements)

References 34 publications

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“…Another example is the sRNA Spot42, which is bound both by Hfq and by CsrA [ 115 , 116 ]. Spot42 post-transcriptionally represses operons that facilitate metabolism of non-preferred carbon sources.…”

Section: Cooperativity Between Chaperones and Other Effector Moleculesmentioning

confidence: 99%

“…Furthermore, Spot42 is not as efficient as CsrB and CsrC in recruiting CsrA, so there is potential for graded effects depending on the relative abundance of these factors. The discovery of the interaction with the Spot42 has opened tantalising possibilities for a new role and mechanism of action of CsrA [ 115 , 116 ].…”

Section: Cooperativity Between Chaperones and Other Effector Moleculesmentioning

confidence: 99%

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Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism

et al. 2022

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In all domains of life, RNA chaperones safeguard and guide the fate of the cellular RNA pool. RNA chaperones comprise structurally diverse proteins that ensure proper folding, stability, and ribonuclease resistance of RNA, and they support regulatory activities mediated by RNA. RNA chaperones constitute a topologically diverse group of proteins that often present an unstructured region and bind RNA with limited nucleotide sequence preferences. In bacteria, three main proteins – Hfq, ProQ, and CsrA – have been shown to regulate numerous complex processes, including bacterial growth, stress response and virulence. Hfq and ProQ have well-studied activities as global chaperones with pleiotropic impact, while CsrA has a chaperone-like role with more defined riboregulatory function. Here, we describe relevant novel insights into their common features, including RNA binding properties, unstructured domains, and interplay with other proteins important to RNA metabolism.

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Section: Cooperativity Between Chaperones and Other Effector Moleculesmentioning

confidence: 99%

Section: Cooperativity Between Chaperones and Other Effector Moleculesmentioning

confidence: 99%

Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism

et al. 2022

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“…Four of them bind to CsrA in vivo (62). In addition, recent studies suggest that CsrA binds sRNAs and promotes sRNA-mRNA complex formation, placing it in the category of RNA chaperones such as Hfq and ProQ (57, 63, 64). Since CsrA works with CsrB to regulate gene expression, we tested the effect of CsrA on MiaA expression.…”

Section: Introductionmentioning

confidence: 99%

Post-transcriptional regulation of the MiaA prenyl transferase by CsrA and the small RNA CsrB inE. coli

Aubee,

Williams,

Adigun

et al. 2024

Preprint

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To determine the role of small RNAs (sRNAs) in the regulation ofmiaA, we constructed a chromosomalmiaA-lacZtranslational fusion driven by the arabinose responsive PBADpromoter and used it to screen against anEscherichia colismall RNA library (containing small RNAs driven by the IPTG inducible PLacpromoter). Our genetic screen and quantitative β-galactosidase assays identified CsrB and its cognate protein CsrA as potential regulators ofmiaAexpression inEscherichia coli. Consistent with our hypothesis that CsrA regulates MiaA post-transcriptional gene expression through binding to the MiaA mRNA 5’ UTR, and CsrB binds and regulates MiaA post-transcriptional gene expression through sequestration of CsrA levels, a deletion ofcsrAsignificantly reduced expression of the reporter fusion as well as reducingmiaAmRNA levels. These results suggest under conditions where CsrA is inhibited, MiaA translation and thus MiaA-dependent tRNA modification may be limiting.IMPORTANCEWe previously demonstrated a role for the i6A modification in the tuning of transcripts for several stress response genes inE. coli. The i6A tRNA modification is catalyzed by the tRNA prenyl transferase encoded by themiaAgene. We set out to identify posttranscriptional regulators of the enzyme necessary for the catalysis of i6A, MiaA, to further understand factors influencing i6A levels in the cell. We identified the CsrA RNA Binding Protein, the CsrB Small RNA, and RNA Degradosome enzymes: RNaseE and PNPase as regulators ofmiaAexpressioin at the post-transcriptional level. Identifying these post-transcripitonal regulators ofmiaAwill help us understand factors influencing i6A levels and may guide future investigations into RNA modifications with regulatory effects on the transcriptome.

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“…The lifetime of bacterial RNA ranges from seconds to an hour (1) and depends on numerous factors, including transcript identity, genotype and growth condition (2). RNA-binding proteins (RBPs) in bacteria include structural components of the ribosome and global post-transcriptional regulators such as Hfq (3, 4) and CsrA (5) which play key roles in modulating translation and RNA stability in concert with a network of small RNAs (sRNAs) (6, 7). Beyond these model RBPs, recent years have seen the discovery of a menagerie of bacterial RBPs that bind hundreds or even thousands of transcripts (8–10), though their functions in shaping the transcriptome remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Improved RNA stability estimation through Bayesian modeling reveals mostSalmonellatranscripts have sub-minute half-lives

Jenniches

Michaux

Reichardt

et al. 2023

Preprint

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RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We develop a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 minute, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with CLIP-seq revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for both proteins in the control of respiration, and for ProQ in the oxidative stress response. Our findings provide new insights into post-transcriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.

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CsrA enters Hfq's territory: Regulation of a base‐pairing small RNA

Cited by 9 publications

References 34 publications

Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism

Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism

Post-transcriptional regulation of the MiaA prenyl transferase by CsrA and the small RNA CsrB inE. coli

Improved RNA stability estimation through Bayesian modeling reveals mostSalmonellatranscripts have sub-minute half-lives

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