ArticleScientific reports2018
A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Modeling binding of the conserved Csr/Rsm protein family across species of the γ-proteobacteria reveals niche-specific adaptation of the post-transcriptional regulon.bioRxiv : the preprint server for biology · 2026Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Post-Transcriptional Regulation of the MiaA Prenyl Transferase by CsrA and the Small RNA CsrB inInternational journal of molecular sciences · 2025Article
- Concentration-Dependent CsrA Regulation of theACS synthetic biology · 2025Article
- Dynamic and intricate regulation by the Csr sRNAs in the Arctic Pseudoalteromonas fuliginea.Communications biology · 2025Article
- Thermodynamic modeling of RsmA - mRNA interactions capture novel direct binding across theFrontiers in molecular biosciences · 2025Article
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- Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.Nature communications · 2024Article
- Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits.Nature communications · 2024Article
- Multitier regulation of theJournal of bacteriology · 2024Article
- The Post-Transcriptional Regulatory Protein CsrA Amplifies Its Targetome through Direct Interactions with Stress-Response Regulatory Hubs: The EvgA and AcnA Cases.Microorganisms · 2024Article
- CsrA Shows Selective Regulation of sRNA-mRNA Networks.bioRxiv : the preprint server for biology · 2023Article
- CsrA selectively modulates sRNA-mRNA regulator outcomes.Frontiers in molecular biosciences · 2023Article
- The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae.PLoS genetics · 2022Article
- RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR.Methods in molecular biology (Clifton, N.J.) · 2022Review
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6 authors.
Funding
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Abstract
Bacterial global post-transcriptional regulators execute hundreds of interactions with targets that display varying molecular features while retaining specificity. Herein, we develop, validate, and apply a biophysical, statistical thermodynamic model of canonical target mRNA interactions with the CsrA global post-transcriptional regulator to understand the molecular features that contribute to target regulation. Altogether, we model interactions of CsrA with a pool of 236 mRNA: 107 are experimentally regulated by CsrA and 129 are suspected interaction partners. Guided by current understanding of CsrA-mRNA interactions, we incorporate (i) mRNA nucleotide sequence, (ii) cooperativity of CsrA-mRNA binding, and (iii) minimization of mRNA structural changes to identify an ensemble of likely binding sites and their free energies. The regulatory impact of bound CsrA on mRNA translation is determined with the RBS calculator. Predicted regulation of 66 experimentally regulated mRNAs adheres to the principles of canonical CsrA-mRNA interactions; the remainder implies that other, diverse mechanisms may underlie CsrA-mRNA interaction and regulation. Importantly, results suggest that this global regulator may bind targets in multiple conformations, via flexible stretches of overlapping predicted binding sites. This novel observation expands the notion that CsrA always binds to its targets at specific consensus sequences.
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