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In vitro turnover numbers do not reflect in vivo activities of yeast enzymes [Systems Biology]
Proceedings of the National Academy of Sciences of the United States of America ( IF 9.4 ) Pub Date : 2021-08-10 , DOI: 10.1073/pnas.2108391118
Yu Chen 1 , Jens Nielsen 2, 3, 4
Affiliation  

Turnover numbers (kcat values) quantitatively represent the activity of enzymes, which are mostly measured in vitro. While a few studies have reported in vivo catalytic rates (kapp values) in bacteria, a large-scale estimation of kapp in eukaryotes is lacking. Here, we estimated kapp of the yeast Saccharomyces cerevisiae under diverse conditions. By comparing the maximum kapp across conditions with in vitro kcat we found a weak correlation in log scale of R2 = 0.28, which is lower than for Escherichia coli (R2 = 0.62). The weak correlation is caused by the fact that many in vitro kcat values were measured for enzymes obtained through heterologous expression. Removal of these enzymes improved the correlation to R2 = 0.41 but still not as good as for E. coli, suggesting considerable deviations between in vitro and in vivo enzyme activities in yeast. By parameterizing an enzyme-constrained metabolic model with our kapp dataset we observed better performance than the default model with in vitro kcat in predicting proteomics data, demonstrating the strength of using the dataset generated here.



中文翻译:

体外周转数不反映酵母酶的体内活性 [系统生物学]

周转数(k cat值)定量地代表酶的活性,其主要在体外测量。虽然一些研究报告了细菌的体内催化速率(k app值),但缺乏对真核生物中k app的大规模估计。在这里,我们估计了酵母酿酒酵母在不同条件下的k app。通过将不同条件下的最大k app与体外k cat进行比较,我们发现R 2 = 0.28 的对数尺度的相关性较弱,这低于大肠杆菌R 2 = 0.62)。弱相关性是由于对通过异源表达获得的酶测量了许多体外k cat值这一事实造成的。去除这些酶改善了与R 2 = 0.41的相关性,但仍不如大肠杆菌,这表明酵母中体外和体内酶活性之间存在相当大的偏差。通过使用我们的k app数据集参数化酶约束代谢模型,我们观察到比使用体外k cat的默认模型在预测蛋白质组学数据方面具有更好的性能,证明了使用此处生成的数据集的优势。

更新日期:2021-08-02
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