Figure 8.

TCDS bias analysis of supercoiling sensitive genes for Escherichia coli and Streptococcus pneumoniae. In (A and B) the TCDS bias z-score for two bacterial species is depicted in depencence on the TCDS range and experimental conditions (see ‘Materials and Methods’ section). The z-score of the difference of the median of TCDS in hyp and rel genes (medianTCDS(hyp)-medianTCDS(rel)) is plotted on the z-axis. Z-scores are based on the TCDS bias between hyp and rel genes relative to the bias for random gene sets. The z-score is coded in color and height. A z-score larger than 2 or smaller than −2, indicating a significant deviation from randomness, is color-coded in red and blue respectively. Hence, a blue color indicates a significantly more negative TCDS at promoters preferring high negative supercoiling than at promoters preferring relaxation. The opposite holds for a red color. In (A) The time axis indicates the 43 different time steps spanning from inoculation (0) over exponential phase (≤120) to stationary phase (≥360) of E. coli In (B) the conditions axis indicates the three replicates of biofilm forming conditions (Bf1-Bf3) and the three replicates of planktonic growth (Pl1-Pl3) of S. pneumoniae. The TCDS range axis shows the TCDS decay parameter of the mathematical model. The longer the TCDS range the slower the decay with distance. At the indicated range the TCDS reaches 1% of its initial strength. (C) A summary of (A and B) for the spatial dependency of the TCDS bias. The mean values along the conditions axis are plotted and normalized by minimum and maximum of each plot.