Figure 3

Differential expression of interacting pathogen cells. (a) Circos plot of SL1344 gene expression for chromosomally-encoded genes as well as plasmid-derived transcripts. The respective coordinates are given in megabases (outmost gray circle) along with the corresponding log₂ fold changes of non-interacting and early interacting, early and mid-level interacting, as well as mid-level and late interacting cells (inner to outer blue circles, respectively). Salmonella pathogenicity islands (SPIs) are highlighted in orange, while other important loci are shown in green. (b,c) Detailed time-dependent expression profiles of selected SL1344 genes. The median-normalized transcript abundance is shown for non-interacting cells along with those from the different interaction stages. PtsN is transcribed as polycistronic mRNA from the chromosome that comprises ten other genes (yrbG, yrbH, yrbI, yrbK, yhbN, yhbG, rpoN, yhbH, yhbJ, and ptsO). The mRNA encoding pefD and the polycistronic mRNA coding for repA, tap, and repA3 are both transcribed from intracellular plasmid pSLT^SL1344. (d) K-means clustering of the time-dependent fold changes from plasmid-encoded transcripts. The corresponding log₂ fold changes were assigned to one of four clusters based on their time-dependent expression patterns. The closest centroid (purple) is shown along with the assigned transcripts (gray) for each cluster. Clustering was performed with Pearson Correlation as distance metric. An accordingly sorted list of the clustered transcripts is provided in Additional file 2: Table S2.