This may allow for faster transport of compounds into the cell or inhibitors out of the cell, allowing the faster growth CB-839 solubility dmso phenotype (Additional file 4). Downregulated genes in the PM in hydrolysate media A change in the environment causes a response of the genetic network which in turn allows efficient plastic adaptation of cellular metabolism to a broad range of unforeseen challenges [46]. Increased transcriptional flexibility allows the cells to address challenges on physiological timescales (not through new mutations) [46]. The PM in 10% v/v Populus hydrolysate decreases the expression of 8 transcription

genes, and in 17.5% v/v Populus hydrolysate it decreases the expression of 22 genes (Additional file 4). In addition the PM in 10% v/v Populus hydrolysate decreases the expression of four genes in the cell defense mechanism category which was determined significant by the odds ratio because of the Selleck GDC-973 small total number of genes being differentially expressed. Cell defense mechanisms and the ability to rapidly change its transcriptional profile in response to changing environments normally contribute to cell fitness; however, these traits may be less advantageous in a steadily-maintained,

pure-culture laboratory environment. As a result, the PM may be decreasing expression of cell defense and transcriptional genes as an energy saving mechanism. Upregulated genes in the WT in hydrolysate medium The WT in hydrolysate medium significantly upregulates two categories of genes that relates very to survival mechanisms: cell defense mechanisms and cell motility genes. The

WT already had a higher expression of the cell defense mechanism genes compared to the PM in standard medium which is further increased in hydrolysate medium. In 10% v/v Populus hydrolysate the WT increased the expression of 38 cellular defense genes compared to standard conditions (Additional file 4). The WT has an average 2-fold higher expression of 8 genes that encode Hedgehog/intein hint domain proteins and 18 phage-associated proteins in hydrolysate medium compared to standard medium. These increases are possibly part of a programmed cell response to the general deterioration of the cell health in hydrolysate conditions. While these increases in gene expression environment may help the cell to survive in a natural environment, they drain resources away from central metabolism and ethanol production. The WT in 10% v/v Populus hydrolysate also increases the expression of 44 cell motility genes and upregulates the expression of sigma factor σD by 3-fold (Table 1). The increase in motility of the WT in response to hydrolysate may be an attempt by the cell to swim away from unfavorable environments (Additional file 4). In contrast, the PM may not see the hydrolysate conditions as an unfavorable environment and further conserves energy by reducing the expression of the cell motility genes.