In vitro turnover numbers do not reflect in vivo activities of yeast enzymes.

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