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Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift.

Rato C, Amirova SR, Bates DG, Stansfield I, Wallace HM - Nucleic Acids Res. (2011)

Bottom Line: Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites.Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects.Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethionine-decarboxylase and antizyme mutants, as well as in the wild-type genetic background.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, UK.

ABSTRACT
The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and spermine by controlling stability of the polyamine biosynthetic enzyme, ornithine decarboxylase. Antizyme mRNA translation depends upon a polyamine-stimulated +1 ribosomal frameshift, forming a complex negative feedback system in which the translational frameshifting event may be viewed in engineering terms as a feedback controller for intracellular polyamine concentrations. In this article, we present the first systems level study of the characteristics of this feedback controller, using an integrated experimental and modeling approach. Quantitative analysis of mutant yeast strains in which polyamine synthesis and interconversion were blocked revealed marked variations in frameshift responses to the different polyamines. Putrescine and spermine, but not spermidine, showed evidence of co-operative stimulation of frameshifting and the existence of multiple ribosome binding sites. Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites. Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects. Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethionine-decarboxylase and antizyme mutants, as well as in the wild-type genetic background.

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Validation of the ribosomal controller frameshift model. (A) Polyamine concentrations were measured in a spe2 mutant with and without SPE1 gene overexpression, in an oaz1 deletant, and in the wild-type strain (putrescine; filled bar, spermidine; light grey, spermine; dark grey). Error bars represent standard deviations (n = 3). (B) Ribosomal frameshift frequencies were measured in the same mutant panel (filled bars) and the intracellular polyamine concentrations measured in the mutants were fed into the frameshift function to predict the frameshift frequency (open bars; error bars represent model uncertainty range originating with variation in the experimental data).
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Figure 5: Validation of the ribosomal controller frameshift model. (A) Polyamine concentrations were measured in a spe2 mutant with and without SPE1 gene overexpression, in an oaz1 deletant, and in the wild-type strain (putrescine; filled bar, spermidine; light grey, spermine; dark grey). Error bars represent standard deviations (n = 3). (B) Ribosomal frameshift frequencies were measured in the same mutant panel (filled bars) and the intracellular polyamine concentrations measured in the mutants were fed into the frameshift function to predict the frameshift frequency (open bars; error bars represent model uncertainty range originating with variation in the experimental data).

Mentions: In the spe2 deletant strain, putrescine accumulated to moderately high levels (6.5 mM; Figure 5A). The measured 4.5% frameshifting was accurately predicted by the model (4.7% frameshift, Figure 5B). Overexpressing the SPE1 gene under the control of the GAL1 promoter in this strain (spe2 pSPE1), produced 65.3 mM intracellular putrescine and a frameshift frequency of 27.4%, again, well approximated by the model (32.4%; Figure 5B). To further validate the model, the oaz1 antizyme deletant was selected, which generates atypical concentrations of all three polyamines (high levels of putrescine and spermidine, normal spermine; Figure 5A), and high levels of frameshifting (21.7%), and which thus tested the ability of the model to integrate the competing polyamine effects. This level of frameshift was accurately predicted by the feedback controller function (21.4%; Figure 5). Finally, we verified that the wild-type frameshift frequency (16.1%) was accurately predicted by the model (13.9%; Figure 5B). The model thus demonstrated an ability to accurately predict the frameshift efficiencies generated by a wide range of different genetic conditions that were typified by markedly different polyamine steady states.Figure 5.


Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift.

Rato C, Amirova SR, Bates DG, Stansfield I, Wallace HM - Nucleic Acids Res. (2011)

Validation of the ribosomal controller frameshift model. (A) Polyamine concentrations were measured in a spe2 mutant with and without SPE1 gene overexpression, in an oaz1 deletant, and in the wild-type strain (putrescine; filled bar, spermidine; light grey, spermine; dark grey). Error bars represent standard deviations (n = 3). (B) Ribosomal frameshift frequencies were measured in the same mutant panel (filled bars) and the intracellular polyamine concentrations measured in the mutants were fed into the frameshift function to predict the frameshift frequency (open bars; error bars represent model uncertainty range originating with variation in the experimental data).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 5: Validation of the ribosomal controller frameshift model. (A) Polyamine concentrations were measured in a spe2 mutant with and without SPE1 gene overexpression, in an oaz1 deletant, and in the wild-type strain (putrescine; filled bar, spermidine; light grey, spermine; dark grey). Error bars represent standard deviations (n = 3). (B) Ribosomal frameshift frequencies were measured in the same mutant panel (filled bars) and the intracellular polyamine concentrations measured in the mutants were fed into the frameshift function to predict the frameshift frequency (open bars; error bars represent model uncertainty range originating with variation in the experimental data).
Mentions: In the spe2 deletant strain, putrescine accumulated to moderately high levels (6.5 mM; Figure 5A). The measured 4.5% frameshifting was accurately predicted by the model (4.7% frameshift, Figure 5B). Overexpressing the SPE1 gene under the control of the GAL1 promoter in this strain (spe2 pSPE1), produced 65.3 mM intracellular putrescine and a frameshift frequency of 27.4%, again, well approximated by the model (32.4%; Figure 5B). To further validate the model, the oaz1 antizyme deletant was selected, which generates atypical concentrations of all three polyamines (high levels of putrescine and spermidine, normal spermine; Figure 5A), and high levels of frameshifting (21.7%), and which thus tested the ability of the model to integrate the competing polyamine effects. This level of frameshift was accurately predicted by the feedback controller function (21.4%; Figure 5). Finally, we verified that the wild-type frameshift frequency (16.1%) was accurately predicted by the model (13.9%; Figure 5B). The model thus demonstrated an ability to accurately predict the frameshift efficiencies generated by a wide range of different genetic conditions that were typified by markedly different polyamine steady states.Figure 5.

Bottom Line: Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites.Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects.Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethionine-decarboxylase and antizyme mutants, as well as in the wild-type genetic background.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, UK.

ABSTRACT
The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and spermine by controlling stability of the polyamine biosynthetic enzyme, ornithine decarboxylase. Antizyme mRNA translation depends upon a polyamine-stimulated +1 ribosomal frameshift, forming a complex negative feedback system in which the translational frameshifting event may be viewed in engineering terms as a feedback controller for intracellular polyamine concentrations. In this article, we present the first systems level study of the characteristics of this feedback controller, using an integrated experimental and modeling approach. Quantitative analysis of mutant yeast strains in which polyamine synthesis and interconversion were blocked revealed marked variations in frameshift responses to the different polyamines. Putrescine and spermine, but not spermidine, showed evidence of co-operative stimulation of frameshifting and the existence of multiple ribosome binding sites. Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites. Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects. Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethionine-decarboxylase and antizyme mutants, as well as in the wild-type genetic background.

Show MeSH
Related in: MedlinePlus