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

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.

Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species