Directed evolution of yeast pyruvate decarboxylase 1 for attenuated regulation and increased stability

Abstract

Five generations of directed evolution resulted in yeast pyruvate decarboxylase 1 (Pdc1) variants with improved activity for 1 mM pyruvate at pH 7.5 in the presence of phosphate. The best variant, named 5LS30, contained the following mutations: A143T, T156A, Q367H, N396I, and K478R. In comparison with native Pdc1, 5LS30 had the substrate concentration required for half-saturation reduced by almost 3-fold at pH 7.5 and the phosphate inhibition reduced by 4-fold at pH 6.0. The apparent cooperativity for pyruvate displayed by 5LS30 was also reduced since it appeared to be activated by pyruvate more easily than the native enzyme. The temperature at which half of the Pdc1 activity was irreversibly lost in 5 min increased from 52.6°C, seen with the native form, to 61.8°C for 5LS30. Curiously, the optimal temperature for Pdc1 activity was found to be dependent upon pyruvate concentration. In 1 mM pyruvate, native Pdc1 performed optimally at 30°C and 5LS30 at 40°C, whereas in 25 mM pyruvate native activity peaked at 45°C and 5LS30 at 55°C. Two screening processes were developed for directed evolution of Pdc1 expressed in Escherichia coli colony screening and culture screening. The latter proved to be an ideal method for isolating PCR-generated variants of the pdc1 gene with the desired phenotype. In this process, cultures were diluted and partitioned within 96-well plates such that each culture aliquot contained an average of two unique genotypes. This allowed rapid preparation of libraries for analysis of activity in crude lysates and can be applied to other directed evolution projects.