Table 2. Validation of the ChIP-Seq data by RT-qPCR.

Expression analysis of the selected genes was performed in a wild type and cbrB mutant strains collected at mid-exponential phase in a minimal medium containing OAA as carbon source. ChIP-Seq enrichment and mRNA levels determined by real-time RT-PCR are shown. Fold change values were calculated dividing the mRNA levels observed in the strain KT2442 by the levels in the cbrB mutant strain (MPO401). A minimum of three biological replicates for each sample in triplicates were performed. Stars designate p-values for the Student's t-test for unpaired samples not assuming equal variance and are referred to the wild type strain. *: p<0.05; **: p<0.01; ***:p<0.005.

ID	Gene-Annotation	ChIP-Seq enrichment	RT-qPCR Fold change	mRNA levels (arbitrary units)		t-test
				KT2442	MPO401
PP0952	rpoN- RNA polymerase sigma-54 factor	2.7	0.1	0.24 ± 0.06	1.78 ± 0.64	1,92E-03	**
PP1206	oprD- basic amino acid specific porin OprD	3.45	0.3	1.71 ± 0.85	5.77 ± 1.64	9,25E-04	***
PP2810	hypothetical protein	2.98	20.6#
PP3009	hypothetical protein	2.61	1.0	0.30 ± 0.09	0.30 ± 0.11	9,74E-01	no differences
PP3074	bhbP- D-beta-hydroxybutyrate permease	7.52	5.7	0.68 ± 0.25	0.12 ± 0.09	7,94E-05	***
PP3420	sensor histidine kinase	3.38	11,7	0.70 ± 0.16	0.06 ± 0.02	8,53E-08	***
PP3656	aromatic compound-specific porin	2.62	1.1	0.015 ± 0.006	0.014 ± 0.003	6,20E-01	no differences
PP4050	glgA- glycogen synthase	2.56	0.7	0.23 ± 0.07	0.33 ± 0.04	9,85E-05	***
PP4391	flgB- flagellar basal-body rod protein FlgB	2.44	4.7	5.87 ± 0.92	1.26 ± 0.17	1,11E-09	***
PP4486	argT- lys/arg/orn ABC transp. substrate-binding protein	2.48	2.8	0.36 ± 0.11	0.13 ± 0.04	2,74E-03	**
PP4643	xanthine/uracil permease family protein	2.7	3.4	0.034 ± 0.01	0.01 ± 0.002	2,31E-03	**
crcZ	CrcZ- regulatory RNA	4.32	43.5	170.39 ± 39.17	3.92 ± 0.52	3,40E-03	**

^# Expression ratio for PP2810 was estimated as the β-galactosidase activity ratio using a transcriptional fusion to lacZ (see Fig 2).