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Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction.

Lavi-Itzkovitz A, Peterman N, Jost D, Levine E - Nucleic Acids Res. (2014)

Bottom Line: Often the sRNA-binding site is adjacent to or overlapping with the ribosomal binding site (RBS), suggesting a possible interplay between sRNA and ribosome binding.Quantitative analysis of these data suggests a recruitment model, where bound ribosomes facilitate binding of the sRNA.Our findings offer a framework for understanding sRNA silencing in the context of bacterial physiology.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

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Three-state model for the interaction between the sRNA, mRNA and ribosomes. (A) Secondary structure of the 5′ end of E. coli sodB mRNA (7,30). Predicted RBS is in bold blue, the interaction region with the sRNA RyhB is in bold red. The start codon is boxed. (B) Three-state model for the mRNA interaction region. Ribosome (a) or sRNA (b) may bind to the transcribed naked mRNAs, leading, respectively, to translation of the mRNA or co-degradation of the sRNA–mRNA complex. Bound ribosomes and the sRNA complex may interact, directly or indirectly (c).
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Figure 1: Three-state model for the interaction between the sRNA, mRNA and ribosomes. (A) Secondary structure of the 5′ end of E. coli sodB mRNA (7,30). Predicted RBS is in bold blue, the interaction region with the sRNA RyhB is in bold red. The start codon is boxed. (B) Three-state model for the mRNA interaction region. Ribosome (a) or sRNA (b) may bind to the transcribed naked mRNAs, leading, respectively, to translation of the mRNA or co-degradation of the sRNA–mRNA complex. Bound ribosomes and the sRNA complex may interact, directly or indirectly (c).

Mentions: In our model (Figure 1B and Supplementary Figure S1) we consider three possible states for the mRNA, depending on the occupation of the interacting region (ribosome-bound, sRNA-bound or naked). Assuming a fast equilibration of the sRNA–mRNA complex, that binding–unbinding of the ribosome to the RBS is rapid and that the reservoir of free ribosomes remains large, the kinetics of the average number of mRNA m, of sRNA s and of protein p follow the set of mass-action equations (see the Supplementary text)(1a)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \frac{{dm}}{{dt}} = \alpha _m - \beta _m m - ks \cdot m \end{equation*}\end{document}(1b)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \frac{{ds}}{{dt}} = \alpha _s - \beta _s s - ks \cdot m \end{equation*}\end{document}(1c)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \frac{{dp}}{{dt}} = \gamma m - \beta _p p \end{equation*}\end{document}with αm and αs being the transcription rate of, respectively, the mRNA and the sRNA, βm, βs and βp the degradation rate of the mRNA, the sRNA and of the protein, k the interaction rate between the sRNA and the mRNA and γ the translation rate of the mRNA. βm, k and γ are coarse-grained parameters accounting for the presence of ribosomes at the interaction site:(2a)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \beta _m = \beta _{m0} \left( {\frac{{1 + wx}}{{1 + x}}} \right) \end{equation*}\end{document}(2b)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} k = k_0 \frac{{(1 + xy)}}{{(1 + x)(1 + z + xyz)}} \end{equation*}\end{document}(2c)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \gamma = \gamma _0 \left( {\frac{x}{{1 + x}}} \right), \end{equation*}\end{document}where x represents the binding affinity of the ribosome and the RBS, w is the ratio between the degradation rates of the ribosome-bound state and the naked state, y is the ratio between the sRNA–mRNA interaction rates in the presence and in the absence of a ribosome at the binding site and z is the ratio between the dissociation rate of the sRNA–mRNA complex and the degradation rate of the complex. These parameters themselves encompass more microscopic underlying processes such as structural rearrangements of the molecules, interactions with the RNA chaperone Hfq (7) and recruitment or activation of RNases (22) (see the Supplementary text). The mean steady-state levels of m, s and p are obtained by setting the temporal derivatives on the left-hand sides of Equations (1a)–(1c) to zero and solving the corresponding set of nonlinear equations.


Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction.

Lavi-Itzkovitz A, Peterman N, Jost D, Levine E - Nucleic Acids Res. (2014)

Three-state model for the interaction between the sRNA, mRNA and ribosomes. (A) Secondary structure of the 5′ end of E. coli sodB mRNA (7,30). Predicted RBS is in bold blue, the interaction region with the sRNA RyhB is in bold red. The start codon is boxed. (B) Three-state model for the mRNA interaction region. Ribosome (a) or sRNA (b) may bind to the transcribed naked mRNAs, leading, respectively, to translation of the mRNA or co-degradation of the sRNA–mRNA complex. Bound ribosomes and the sRNA complex may interact, directly or indirectly (c).
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Figure 1: Three-state model for the interaction between the sRNA, mRNA and ribosomes. (A) Secondary structure of the 5′ end of E. coli sodB mRNA (7,30). Predicted RBS is in bold blue, the interaction region with the sRNA RyhB is in bold red. The start codon is boxed. (B) Three-state model for the mRNA interaction region. Ribosome (a) or sRNA (b) may bind to the transcribed naked mRNAs, leading, respectively, to translation of the mRNA or co-degradation of the sRNA–mRNA complex. Bound ribosomes and the sRNA complex may interact, directly or indirectly (c).
Mentions: In our model (Figure 1B and Supplementary Figure S1) we consider three possible states for the mRNA, depending on the occupation of the interacting region (ribosome-bound, sRNA-bound or naked). Assuming a fast equilibration of the sRNA–mRNA complex, that binding–unbinding of the ribosome to the RBS is rapid and that the reservoir of free ribosomes remains large, the kinetics of the average number of mRNA m, of sRNA s and of protein p follow the set of mass-action equations (see the Supplementary text)(1a)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \frac{{dm}}{{dt}} = \alpha _m - \beta _m m - ks \cdot m \end{equation*}\end{document}(1b)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \frac{{ds}}{{dt}} = \alpha _s - \beta _s s - ks \cdot m \end{equation*}\end{document}(1c)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \frac{{dp}}{{dt}} = \gamma m - \beta _p p \end{equation*}\end{document}with αm and αs being the transcription rate of, respectively, the mRNA and the sRNA, βm, βs and βp the degradation rate of the mRNA, the sRNA and of the protein, k the interaction rate between the sRNA and the mRNA and γ the translation rate of the mRNA. βm, k and γ are coarse-grained parameters accounting for the presence of ribosomes at the interaction site:(2a)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \beta _m = \beta _{m0} \left( {\frac{{1 + wx}}{{1 + x}}} \right) \end{equation*}\end{document}(2b)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} k = k_0 \frac{{(1 + xy)}}{{(1 + x)(1 + z + xyz)}} \end{equation*}\end{document}(2c)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} \gamma = \gamma _0 \left( {\frac{x}{{1 + x}}} \right), \end{equation*}\end{document}where x represents the binding affinity of the ribosome and the RBS, w is the ratio between the degradation rates of the ribosome-bound state and the naked state, y is the ratio between the sRNA–mRNA interaction rates in the presence and in the absence of a ribosome at the binding site and z is the ratio between the dissociation rate of the sRNA–mRNA complex and the degradation rate of the complex. These parameters themselves encompass more microscopic underlying processes such as structural rearrangements of the molecules, interactions with the RNA chaperone Hfq (7) and recruitment or activation of RNases (22) (see the Supplementary text). The mean steady-state levels of m, s and p are obtained by setting the temporal derivatives on the left-hand sides of Equations (1a)–(1c) to zero and solving the corresponding set of nonlinear equations.

Bottom Line: Often the sRNA-binding site is adjacent to or overlapping with the ribosomal binding site (RBS), suggesting a possible interplay between sRNA and ribosome binding.Quantitative analysis of these data suggests a recruitment model, where bound ribosomes facilitate binding of the sRNA.Our findings offer a framework for understanding sRNA silencing in the context of bacterial physiology.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

Show MeSH
Related in: MedlinePlus