Fig. 2: Selection of promoter and terminator GEM-blocks with diverse activity. | Nature Communications

Fig. 2: Selection of promoter and terminator GEM-blocks with diverse activity.

From: Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast

Fig. 2

a yECitrine fluorescence regulated by 13 hybrid promoters (TDH3 core promoter preceded by a LoxPsym-flanked UPE, yellow), in combination with terminator CYC1. Gray bars indicate natural promoters of the corresponding UPEs. Selected 5’ GEM-blocks are indicated in bold. Bars and error bars represent average and standard deviation of three biological replicates, respectively. Unpaired two-sample two-sided t tests to compare the hybrid and native promoters, with p = 1.21e-06 (ADH1), 1.29e-07 (RPL18B), 4.89e-06 (CYC1), 0.001845 (RNR2), 2.07e-05 (ALD6), 3.69e-07 (RPL10), 0.003511 (RPL13B), 1.76e-06 (ENO2), 0.001156 (CCW12), 0.006358 (PGK1), 0.0002717 (TPI1), 5.44e-05 (PGI1) and 0.001312 (TDH3). b Activity of hybrid promoters in 11 different media (y-axis), represented by z-score of normalized fluorescence levels of three biological replicates, calculated by medium. c Pearson correlation test between yECitrine fluorescence and mRNA abundance (ΔCT value) of selected 5’ GEM-blocks (R2 = 0.82, p = 0.0021). Dots, horizontal and vertical error bars represent average, standard error and standard deviation of three biological replicates, respectively. Colors (shades of purple, blue and green) correspond to the UPE element used in the hybrid promoter with the TDH3 core. Gray represents the TDH3 core promoter by itself and black the native TDH3 promoter. d yECitrine fluorescence regulated by the TPI1 promoter and 10 terminator sequences, either flanked by LoxPsym sites (yellow) or not (gray). Selected 3’ GEM-blocks are indicated in bold. Bars and error bars represent average and standard deviation of three biological replicates, respectively. Unpaired two-sample two-sided t tests to compare LoxPsym-flanked and natural terminator sequences with p = 0.07434 (ACS2), 2.23e-05 (GRE3), 0.0271 (TPS1), 1.80e-06 (VPS13), 5.86e-07 (IDP1), 0.02329 (ACS1), 4.91e-07 (SPG5), 0.000103 (TPI1), 0.176 (CYC1), 0.004445 (HIS5). e LoxPsym-flanked terminator activities in 11 different media (y-axis), represented by z-scores of normalized fluorescence levels of three biological replicates, calculated by medium. f yECitrine fluorescence versus mRNA abundance of selected 3’ GEM-blocks (Pearson correlation test with R2 = 0.89, p = 0.0046). Dots, horizontal and vertical error bars represent average, standard error and standard deviation of three biological replicates, respectively. Color corresponds to LoxPsym-flanked terminator. Source data are provided as a Source Data file.

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