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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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Competing models for sRNA–ribosome interactions yield qualitatively different predictions. Model predictions of the sRNA efficacy (fold-repression in gene expression) as a function of the translational activity for the competition (y = 0.01, green lines) and the recruitment modes (y = 100, blue lines) in the crossover (αs/αm = 1, dashed lines) or silenced (αs/αm = 2, full lines) regimes. Fixed parameters are (in min−1) k0 = 0.04, αm = 1, βs = 0.1, βm0 = 0.4, w = 1, z = 0.001.
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Figure 2: Competing models for sRNA–ribosome interactions yield qualitatively different predictions. Model predictions of the sRNA efficacy (fold-repression in gene expression) as a function of the translational activity for the competition (y = 0.01, green lines) and the recruitment modes (y = 100, blue lines) in the crossover (αs/αm = 1, dashed lines) or silenced (αs/αm = 2, full lines) regimes. Fixed parameters are (in min−1) k0 = 0.04, αm = 1, βs = 0.1, βm0 = 0.4, w = 1, z = 0.001.

Mentions: Model predictions plotted in Figures 2 and 5A were calculated using typical parameter values of bacterial sRNA pathways (27). Fixed parameters are (in min−1) .


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)

Competing models for sRNA–ribosome interactions yield qualitatively different predictions. Model predictions of the sRNA efficacy (fold-repression in gene expression) as a function of the translational activity for the competition (y = 0.01, green lines) and the recruitment modes (y = 100, blue lines) in the crossover (αs/αm = 1, dashed lines) or silenced (αs/αm = 2, full lines) regimes. Fixed parameters are (in min−1) k0 = 0.04, αm = 1, βs = 0.1, βm0 = 0.4, w = 1, z = 0.001.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231754&req=5

Figure 2: Competing models for sRNA–ribosome interactions yield qualitatively different predictions. Model predictions of the sRNA efficacy (fold-repression in gene expression) as a function of the translational activity for the competition (y = 0.01, green lines) and the recruitment modes (y = 100, blue lines) in the crossover (αs/αm = 1, dashed lines) or silenced (αs/αm = 2, full lines) regimes. Fixed parameters are (in min−1) k0 = 0.04, αm = 1, βs = 0.1, βm0 = 0.4, w = 1, z = 0.001.
Mentions: Model predictions plotted in Figures 2 and 5A were calculated using typical parameter values of bacterial sRNA pathways (27). Fixed parameters are (in min−1) .

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