Transcriptome guided metabolic engineering – Analysis.

Affymetrix Yeast 2.0 DNA microarrays were used for transcriptome analysis of each strain cultured in well-controlled glucose batch fermentations. The top 2000 differentially expressed genes had an adjusted p.value<0.01 and log-fold change (lfc)>0.5. A carbon-limited and nitrogen-limited chemostat transcriptome data set using the reference strain, surveyed at dilution rates (D) of 0.03, 0.1, and 0.2 h−1 was used to determine which genes are growth-related under each condition. A total of 36 unique growth-related genes were identified from statistical analysis of each data set and with a total of 8 growth-related genes being among the top 20 differentially expressed genes between the reference and evolved 8D strain. After removal of the 36 genes, a total of 1964 genes were carried further for pathway analysis.