Table 1.

Expression levels of 13 differentially expressed genes between a typical E. coli strain (EDL933) and EIEC/Shigella strains

In vitro grown bacteria
EDL933 (E)
EIEC
S. sonnei (SS)
In vivo grown bacteria
Gene
Functional group
Mean
SD
Mean
SD
Mean
SD
Ratio
P-value
S. flexneri (S3)
hrpB Transcription, RNA processing and degradation 0.83 0.09 2.22 0.45 2.61 0.34 2.9 5.2E-06* 1-10
fhuC Transport and binding proteins 0.12 0.03 0.34 0.06 0.18 0.01 2.1 1.1E-03 1-10
entD Biosynthesis of cofactors, prosthetic groups and carriers 0.37 0.02 0.44 0.02 0.47 0.00 1.2 8.5E-04 10-100
ybeA Hypothetical, unclassified, unknown 0.33 0.04 0.79 0.14 0.68 0.04 2.3 6.5E-04 1-10
nagE Transport and binding proteins 2.48 0.68 9.54 3.21 6.44 2.31 3.2 5.5E-03 0.1-1
fruB Transport and binding proteins 0.10 0.00 0.47 0.03 0.35 0.13 4.3 7.6E-04 1-10
exbD Transport and binding proteins 0.13 0.02 0.51 0.04 0.31 0.05 3.1 2.1E-03 10-100
deaD Transcription, RNA processing and degradation 0.59 0.05 3.20 0.36 2.82 1.33 5.1 6.7E-05* 10-100
bioH Biosynthesis of cofactors, prosthetic groups and carriers 0.36 0.06 0.93 0.26 1.01 0.08 2.7 1.7E-04 1-10
yhiP Transport and binding proteins 3.79 0.40 21.87 3.65 12.18 3.64 4.5 3.4E-03 0.1-1
uhpC Transport and binding proteins 0.09 0.03 0.28 0.05 0.22 0.03 2.8 4.0E-04 10-100
uhpB Transport and binding proteins 0.01 0.00 0.15 0.06 0.12 0.01 9.3 5.9E-04 10-100
yiiT
Putative regulatory proteins
17.04
0.39
11.59
0.02
11.91
0.18
0.7
5.3E-04
0.1-1

[i] Genes are listed as in Table S1 according to their physical position on the K12-MG1655 chromosome. For in vitro grown bacteria, values were normalized on dinB expression level. For each gene, ratio value corresponds to the EIEC/Shigella expression level mean to the EDL933 expression level. Student t test P values were calculated between the EDL933 and the EIEC/Shigella expression levels. (*) Genes for which RT-PCR was repeated six times. For other genes, RT-PCR was repeated three to four times. For in vivo grown bacteria, expression levels are given as a range of magnitude of the expression level ratio between Shigella strain either infecting eukaryotic cells or in vitro growing. All genes were found overexpressed in EIEC/Shigella strains except yiiT gene, which is underexpressed in these strains, as observed in the macroarray analysis. The genes involved in iron acquisition process are indicated in bold.