Figure 1.
Workflow of the fermentation genomics platform.
L. plantarum WCFS1 is fermented under different conditions and samples derived from these fermentations are assessed at the molecular level by full genome transcriptome profiling and in parallel the physiological characteristics of the fermentations are determined. The datasets obtained are stored in FermDB and correlated. Figure adapted from [8].
Table 1.
Fermentation conditions and physiological characteristics of L. plantarum WCFS1 recorded for the 30 fermentors performed.
Table 2.
Mann-Whitney U-based correlation of fermentation parameters and physiological characteristics.
Figure 2.
Box plots of the significant correlations in Table 2.
Figure 3.
Citrate (dark bars) and succinate (light bars) concentrations in the 29 fermentations.
Fermentors marked with an asterisk represent fermentations to which 0.3 M NaCl was added.
Figure 4.
Simpheny-based visualization of the metabolic map of L. plantarum WCFS1 reveals the interconnectivity of the pentose phosphate pathway, and teichoic acid and nucleotide biosynthesis to citrate and succinate levels.
Arrows indicate reaction and their up- or downregulation (p<0.05 in green and red, respectively) in the increased citrate uptake and succinate production conditions. Marked with boxes next to the reaction names is the average importance per gene involved in the reaction for the two classifications (citrate and succinate). Bar heights correspond to importance levels.
Figure 5.
Scatterplot of the µmax and expression level of the highly correlated genes.
Each diamond symbol in the plot corresponds to a single fermentation or which both µmax and microarray data was determined. Expression levels were normalized (see methods) and averaged. Correlation of µmax and transcriptome data is 0.95 (Spearman rank).
Figure 6.
Reconstruction of the transcriptome response clouds to (combinations of) different fermentation parameters.
Nodes in the network correspond to the fermentation parameters (in blue) and the genes with significant (p<0.05) altered (ratio change >2) expression level (light red). Each gene for which gene expression is significantly altered by changing the fermentation parameter is connected to that fermentation parameter by an edge. Edge colour reflects under which condition the gene has the (relatively) highest expression (red = low temperature, [NaCl], [AA], pH or O2 levels or green = high temperature, [NaCl], [AA], pH or O2 levels). Visualization of the network was performed in cytoscape (http://cytoscape.org). Genes are grouped on the basis of shared response with the different fermentation variables. In the lower panel the response cloud of O2 is shown in more detail, in combination with a web logo of the putative TF binding site. Genes that share this binding site in their upstream sequence have been colored yellow.