Supporting Information

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Supporting Figure 5
Supporting Table 1
Supporting Table 2
Supporting Table 3
Supporting Figure 6
Supporting Table 4
Supporting Figure 7

Fig. 5. Representative electrophoretograms of total RNA extracted from an in vitro culture (A) and from the bubo of a rat with terminal plague (B). Prokaryotic and eukaryotic rRNA peaks are indicated.

Fig. 6. Differential expression in the bubo of Y. pestis genes encoding metabolic pathways. Enzymatic reactions predicted to be up-regulated and down-regulated in the bubo compared with in vitro culture are indicated by red and blue arrows, respectively. Differential transcription (fold difference) in the bubo relative to different in vitro growth conditions is indicated by the color scale in the row of four boxes next to each gene, in the order (left to right): exponential phase, 21°C; stationary phase, 21°C; exponential phase, 37°C; stationary phase, 37°C.

Fig. 7. Real-time reverse transcription (RT)-PCR confirmation of microarray results. Microarray results for 12 Y. pestis genes were verified by TaqMan RT-PCR. The quantity of each mRNA was determined relative to that of the reference gene crr (YPO2995, encoding a phosphotransferase system component), whose array expression level was not affected by in vivo or in vitro growth condition. Fold differences in transcript levels of the 12 Y. pestis genes in the bubo compared with exponential (A and C) or stationary (B and D) phase in vitro cultures grown at 37°C (A and B) or 21°C (C and D) are shown as determined by microarray (gray bars) and RT-PCR (black bars).