A systems approach to model natural variation in reactive properties of bacterial ribosomes
A systems approach to model natural variation in reactive properties of bacterial ribosomes
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DOI：
10.1186/1752-0509-2-62
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发表时间：
2008-07-13
影响因子：
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通讯作者：
Herring, Patricia A.
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文献类型：
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作者：
Jackson, Julius H.;Schmidt, Thomas M.;Herring, Patricia A.
背景：细菌和古生菌中翻译蛋白质输出的自然变化可能是核糖体的生物特异性。本文采用系统方法来模拟蛋白质输出，作为核糖体介导的翻译装置中特定核糖体反应特性的测量。我们使用稳态假设来定义核糖体的过渡态复合体，加上mRNA， tRNA，氨基酸和反应因子，作为一个子系统，允许将重点放在完成的翻译输出上，作为核糖体特定特性的测量。结果：与酶复合物的稳态反应类似，我们提出了一个来自任何基因的mRNA的稳态翻译复合物，并得出了最大特异性翻译活性T-a(max)，作为核糖体反应复合物的特性。T-a（max）具有每个特定mRNA每次a蛋白输出的单位。核糖体的一个相关特性是(T) /波浪（A (max)），每个总RNA的A蛋白单位为(T) /波浪(A (max)) = rho A T- A (max)，其中rho(A)表示从基因A信息中翻译P-a的总RNA的比例。作为核糖体性质的T-a（max）类似于纯化酶的k(cat)，而(T) / tilde （a(max)）类似于粗提取物中的酶比活性。结论：通过类比酶反应复合体，我们建立了一个核糖体反应模型来测量细菌核糖体的特异性翻译活性。我们建议使用该模型来设计实验测试我们的假设，即特定翻译活性是一种核糖体特性，受自然变异和自然选择的影响，就像任何特定酶的V-max和K-m一样。
Background: Natural variation in protein output from translation in bacteria and archaea may be an organism-specific property of the ribosome. This paper adopts a systems approach to model the protein output as a measure of specific ribosome reactive properties in a ribosome-mediated translation apparatus. We use the steady-state assumption to define a transition state complex for the ribosome, coupled with mRNA, tRNA, amino acids and reaction factors, as a subsystem that allows a focus on the completed translational output as a measure of specific properties of the ribosome.Results: In analogy to the steady-state reaction of an enzyme complex, we propose a steady-state translation complex for mRNA from any gene, and derive a maximum specific translation activity, T-a(max), as a property of the ribosomal reaction complex. T-a(max) has units of a-protein output per time per a-specific mRNA. A related property of the ribosome, (T) over tilde (a(max)), has units of a-protein per time per total RNA with the relationship (T) over tilde (a(max)) = rho a T-a(max), where rho(a) represents the fraction of total RNA committed to translation output of P-a from gene a message. T-a(max) as a ribosome property is analogous to k(cat) for a purified enzyme, and (T) over tilde (a(max)) is analogous to enzyme specific activity in a crude extract.Conclusion: Analogy to an enzyme reaction complex led us to a ribosome reaction model for measuring specific translation activity of a bacterial ribosome. We propose to use this model to design experimental tests of our hypothesis that specific translation activity is a ribosomal property that is subject to natural variation and natural selection much like V-max and K-m for any specific enzyme.