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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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Related in: MedlinePlus

Antizyme ribosomal frameshifting and readthrough in wild-type BY4741 and spe1 spe2 paa1 fms1 deletant strains. Average percent frameshifting (FS) and readthrough (RT) for wild-type and quadruple deletant strains grown in polyamine-free media. Filled bars represent average frameshift and open bars represent readthrough. Standard deviations are presented for all bars (typically <15% of mean value; n = 3).
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Figure 2: Antizyme ribosomal frameshifting and readthrough in wild-type BY4741 and spe1 spe2 paa1 fms1 deletant strains. Average percent frameshifting (FS) and readthrough (RT) for wild-type and quadruple deletant strains grown in polyamine-free media. Filled bars represent average frameshift and open bars represent readthrough. Standard deviations are presented for all bars (typically <15% of mean value; n = 3).

Mentions: In order to understand how polyamines govern yeast antizyme synthesis, we analysed in vivo how each of the different polyamines affect the three mutually exclusive processes of frameshifting, readthrough and termination at the antizyme frameshift site in the quadruple deletant yeast. Frameshift and readthrough were measured in actively growing wild-type and spe1 spe2 paa1 fms1 cultures using dicistronic reporter plasmids containing the antizyme frameshift site, along with readthrough controls (‘Materials and Methods’ section). In the absence of added polyamines, ∼16.1% of the translating ribosomes shifted to the +1 frame in the wild-type genetic background, and only 3.7% in the quadruple deletant (Figure 2). The readthrough frequencies for both wild-type and quadruple deletant strains were similar and low (0.52 and 0.43%, respectively; Figure 2). Thus frameshifting, but not stop codon readthrough, appears to be polyamine sensitive.Figure 2.


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)

Antizyme ribosomal frameshifting and readthrough in wild-type BY4741 and spe1 spe2 paa1 fms1 deletant strains. Average percent frameshifting (FS) and readthrough (RT) for wild-type and quadruple deletant strains grown in polyamine-free media. Filled bars represent average frameshift and open bars represent readthrough. Standard deviations are presented for all bars (typically <15% of mean value; n = 3).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113565&req=5

Figure 2: Antizyme ribosomal frameshifting and readthrough in wild-type BY4741 and spe1 spe2 paa1 fms1 deletant strains. Average percent frameshifting (FS) and readthrough (RT) for wild-type and quadruple deletant strains grown in polyamine-free media. Filled bars represent average frameshift and open bars represent readthrough. Standard deviations are presented for all bars (typically <15% of mean value; n = 3).
Mentions: In order to understand how polyamines govern yeast antizyme synthesis, we analysed in vivo how each of the different polyamines affect the three mutually exclusive processes of frameshifting, readthrough and termination at the antizyme frameshift site in the quadruple deletant yeast. Frameshift and readthrough were measured in actively growing wild-type and spe1 spe2 paa1 fms1 cultures using dicistronic reporter plasmids containing the antizyme frameshift site, along with readthrough controls (‘Materials and Methods’ section). In the absence of added polyamines, ∼16.1% of the translating ribosomes shifted to the +1 frame in the wild-type genetic background, and only 3.7% in the quadruple deletant (Figure 2). The readthrough frequencies for both wild-type and quadruple deletant strains were similar and low (0.52 and 0.43%, respectively; Figure 2). Thus frameshifting, but not stop codon readthrough, appears to be polyamine sensitive.Figure 2.

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