TABLE 3.

Carbon metabolic genes identified in ChIP-chip analysis^a

Gene ID	Gene name	Enrichment factorb	DNA microarray ratioc	GntR1 binding motif (5′–3′)	Function
cgR_1513	gnd	5.66	3.65	AAAGGTGTGACCATT	6-Phosphogluconate dehydrogenase
cgR_2397	gntV	5.19	60.60	ATTGGTACTATCATA	Gluconate kinase
cgR_1973	pyk	5.14	1.34	ACAGGTACTACCATT	Pyruvate kinase
cgR_0261	iolT1	5.06	0.74	ATTGGTAATACTTAG	Metabolite transport protein
cgR_0402	bglS	5.01	10.72	AAAGGGATTACCATT	Putative beta-glucosidase
cgR_2751	pckA	4.91	0.42	AAAGGGATTACCATT	Phosphoenolpyruvate carboxykinase
cgR_2895	maeB	4.67	0.48	AATGATATGACCATC	Malic enzyme
cgR_2262	mdh	4.64	0.85	GATGGTGTTACCTTT	Malate dehydrogenase
cgR_1425	ptsG	4.54	0.29	AAAAGTATTACCTTT	Phosphotransferase, glucose-specific enzyme II
cgR_1624	tkt	4.46	1.82	AAAGGTGTGACCAAT	Transketolase
cgR_2806	gntP	4.32	2.79	ATTAGTATGATCAAA	Gluconate permease
cgR_2497	dctA	4.25	4.17	ATTAATATTACCTTT	Na+/H+-dicarboxylate symporter
cgR_1636	gapA	4.24	1.23	ATTGGGATTACCATT	Glyceraldehyde-3-phosphate dehydrogenase
cgR_2454		4.20	9.01	TTAGGTGTGATCTTT	Sugar phosphate isomerase/epimerase
cgR_1038	gapB	4.14	0.31	AAAGATGTGATCATT	Glyceraldehyde 3-phosphate dehydrogenase
cgR_2451		3.91	2.40	ATTAGTGTGACCAAA	Na+/H+-dicarboxylate symporter
cgR_2222	dctP1	3.49	7.77	AAAGGGATCACCATT	Putative C4-dicarboxylate-binding protein
cgR_2896	gntK	3.18	1.83	AAAGGTCTGACTAAT	Putative gluconate kinase
cgR_2120	aceE	3.09	0.95	TTAGGTACGACCAAA	Pyruvate dehydrogenase
cgR_0784	icd	2.52	1.07	CTTGGTGTGATCTTT	Isocitrate dehydrogenase
cgR_2547	ptsS	2.29	1.69	AATAGTGCCACCTTT	Enzyme II sucrose protein

^aAll ChIP-chip peaks were located upstream of the genes listed in the Gene ID column.

^bRelative peak height ratios of the array data in the ChIP DNA to input DNA are shown in the base 2 logarithm.

^cRelative ratios of the transcript levels in the gntR1-deleted cells to those in the wild-type strain were determined by DNA microarray analysis.