Figure 4.

Bile tolerance. (A) With genes divided into functional classes based on the S. Typhi CT18 annotation, the observed number of different transposon insertion sites per functional gene class is expressed as a proportion of the insertion sites expected if sites were distributed randomly for growth in the presence or absence of bile (abbreviations as in Fig. 3). Values greater than 1 indicate that insertions into the gene class are better tolerated, while values less than 1 indicate that insertions into the gene class are more poorly tolerated. (B) Data from A plotted to show how much the proportion of expected differs between LB (no bile) and bile (LB supplemented with 10% ox bile). A positive value indicates more insertions than expected in LB relative to bile; a negative value indicates fewer insertions than expected in LB relative to bile. (C) Detailed plot generated using Artemis (Rutherford et al. 2000), comparing the frequency and distribution of transposon directed insertion site sequence reads across the O-antigen biosynthesis (wba) genes following growth in the absence (top distribution) or presence (bottom distribution) of ox bile. The y-axis shows the number of mapped sequence reads within a window size of 3. The maximum number of sequence reads within each plot is shown top right. After growth in the presence of ox bile the number of transposon insertions is much reduced in this region. (D) Similar to (C), showing the frequency and distribution of sequence reads in and adjacent to the pagP gene.