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. 2008 Oct 10;190(24):8033–8044. doi: 10.1128/JB.00705-08

TABLE 3.

Genes enriched in SugRStrep-DNA complexes identified by ChIP-to-chip analysisa

Gene IDb Gene name, gene product, and/or deduced function ChIP-to-chip enrichment factor with:
Glucose Fructose Sucrose LB
cg0641 fabG2, probable short-chain dehydrogenase, secreted 4.27 3.41 3.25 13.62
cg0682 Predicted ATPase or kinase 2.77 2.50 2.65 8.91
cg1110 Conserved hypothetical protein 5.07 6.51 7.26 8.58
cg1111 eno, enolase 4.27 4.72 4.60 10.64
cg1408 Hypothetical membrane protein 2.01 2.14 1.06 6.35
cg2157P terC, membrane protein TerC 2.76 2.60 2.52 7.75
cg3068P fba, fructose-1,6-bisphosphate aldolase 4.12 3.76 3.46 28.24
cg3219 ldhA, l-lactate dehydrogenase 2.81 3.93 2.35 4.28
cg0441P lpd, diaminolipoamide dehydrogenase 1.38 1.23 0.95 3.97
cg0448 Hypothetical protein 1.12 1.10 1.07 2.07
cg1174P tkt, transketolase 1.93 1.36 1.18 7.28
cg1283 aroE2, putative Shikimate/Quinate 5-dehydrogenase 1.17 1.23 0.98 2.39
cg1493 Conserved hypothetical protein 1.13 0.99 1.05 3.58
cg1537P ptsG, glucose-specific IIABC PTS component 1.24 1.13 0.98 3.79
cg1696 Permease of the major facilitator superfamily 1.34 1.29 1.07 4.80
cg2115P sugR, transcriptional regulator DeoR family 1.30 1.45 1.45 4.39
cg2121 ptsH, phosphocarrier protein HPr 1.91 1.87 1.47 9.64
cg2262P ftsY, signal recognition particle GTPase 1.29 1.10 1.07 2.55
cg2291 pyk, pyruvate kinase 1.32 1.26 1.12 2.41
cg2794 Conserved hypothetical protein 1.33 1.26 1.45 3.49
cg2831P-cg2833P ramA, transcriptional regulator LuxR-family/cysK, cysteine synthase 1.22 1.28 1.51 2.47
cg2908 Hypothetical trehalose-binding protein 1.46 1.29 0.98 2.85
cg2909 otsB, trehalose-phosphatase 1.56 1.48 1.39 4.48
cg3366 sgcA, putative phosphotransferase enzyme II, A component 1.12 1.19 1.74 2.33
cg0974 Conserved hypothetical protein 1.43 3.15 0.80
cg1074 Conserved hypothetical protein 2.30 1.83 0.25 2.71
cg1142 Na+/proline, Na+/panthothenate symporter 2.03 1.06
a

Genes or genomic regions listed showed enrichment factors of two or more in three independent ChIP-to-chip analyses during growth on LB (P ≤ 0.05). DNA enriched in SugRStrep-DNA complexes by a factor of two or more was considered as a candidate target bound by SugR in vivo. In addition, those genes which were enriched in three additional ChIP-to-chip experiments during growth on CgXII minimal medium containing 100 mM glucose, 100 mM fructose, or 50 mM sucrose are listed.

b

P, enrichment factors based on intergenic regions, of which few were present on the DNA microarray.