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. 2012 Dec 11;3(6):e00407-12. doi: 10.1128/mBio.00407-12

TABLE 1 .

ChIP-chip targets involved in primary (selected) and secondary metabolism

Region
bounda 		Enrichment
ratiob 		Regulated
genec 		Predicted function
of regulated gene		 Distanced Predicted
binding sitee
Secondary metabolism
    SCO0380-0381 2.38 SCO0381 Glycosyltransferase; deoxysugar synthesis −401 GTCGAACTCGGCAC (−371)
    SCO0381 2.04 SCO0381 Glycosyltransferase; deoxysugar synthesis 186 GTGACCACCGCCGT (186)
    SCO1273 1.96 SCO1273 Reductase in type II fatty acid synthase 650 CTGCCGGTGGGCAC (736)
    SCO1273-1274 2.07 SCO1273 Reductase in type II fatty acid synthase −94 GTGGCAGATTTCTG (−81)
    SCO3217f 3.2 SCO3217 CdaR, pathway-specific activator; CDA synthesis 847 GCGGAGGCACTCAC (710)
    SCO3229f 2.81 SCO3229 HmaS, 4-hydroxymandelate synthase 90 GTGACATCGCGTAC (56)
    SCO3230f 2.03 SCO3230 CdaPSI, CDA peptide synthetase I 282 GGGGTGCCGTACAC (286)
    SCO5084g 1.86 SCO5084 ActII-3, actinorhodin export 1706 CTGTCCTTCTTCAC (1,645)
    SCO5085 (1)g 2.77 SCO5085 ActII-4, pathway-specific activator; Act synthesis 358 GTGACGAGCGACGA (234)
    SCO5085 (2)g 1.6 SCO5085 ActII-4, pathway-specific activator; Act synthesis 38 GTCCATGTAATCAC (24)
    SCO5221-SCO5222 2.89 SCO5222 EizA lyase, sesquiterpene cyclase −177 GTTCGTCTGTGCAC (−185)
    SCO5222 (1) 3.01 SCO5222 EizA lyase, sesquiterpene cyclase 896 GAGGAATGCATCAC (847)
    SCO5222 (2) 2.88 SCO5222 EizA lyase, sesquiterpene cyclase 356 GTGACATCGTCCAC (317)
    SCO5223 2.47 SCO5223 Putative cytochrome P450, sesquiterpene cyclase 736 GTCGCGATACTCAC (810)
    SCO5881 (1)h 2.44 SCO5881 RedZ, pathway-specific activator; Red synthesis 130 GCCCCCCTCTTCAC (166)
    SCO5881 (2)h 2.16 SCO5881 RedZ, pathway-specific activator; Red synthesis 590 GTCTCGCCCACCAC (520)
    SCO6271-SCO6272i 1.83 SCO6271 AccA1, acyl-CoA carboxylase complex; yCPK synthesis −51 GTGAGGAGAATCTT (−8)
SCO6272 Scf, secreted FADj-binding protein, yCPK synthesis −257 AAGATTCTCCTCAC (−300)
    SCO6272i 2.06 SCO6272 Scf, secreted FAD-binding protein, yCPK synthesis 43 GTGTCCGGCGGCGC (49)
    SCO6275-SCO6276i 1.8 SCO6275 CpkA, type I polyketide synthase; yCPK synthesis −68 CCGAGCGTGGTCAC (0)
SCO6276 Monooxygenase; yCPK synthesis −257 GTGACCACGCTCGG (−180)
    SCO6276i 2.13 SCO6276 85 GTGGTAACTGCCGC (91)
    SCO6283i 1.81 SCO6283 Nucleoside-diphosphate-sugar epimerase; yCPK synthesis 136 CTGGACGAGTCCAC (136)
SCO6282 3-Oxoacyl-[acyl-carrier protein] reductase; yCPK synthesis −253 GTGGACTCGTCCAG (−253)
    SCO6429 2.27 SCO6429 Putative NRPS 139 GTGAAGGCGCCCTG (87)
Primary metabolism (selected)
    SCO4561-4562 2.67 SCO4562 NuoA, NADH dehydrogenase subunit −326 GTGAAAATGTCAC (−281)
    SCO4921-4922 1.97 SCO4921 AccA2, acyl-CoA carboxylase complex A subunit −117 GTGTGGGCAAGCTCAC (−80)
    SCO4978-4979 1.77 SCO4979 PckA, phosphoenolpyruvate carboxykinase −33 GTCGCAGCCCCCAC (−45)
    SCO5260-5261 2.26 SCO5261 NADP+-dependent malic enzyme −129 GTGGCCCAGACAG (−89)
a

 Genomic context of Crp-associated sequences.

b

 Crp-DNA interaction affinity.

c

 Genes regulated by Crp-associated sequences.

d

 Distances from the center of Crp-associated sequences to the start codons of regulated genes. Negative values indicate sites upstream of start codons while positive values indicate sites within open reading frames.

e

 Numbers in parentheses are distances to the start codon of regulated genes, as described in footnote d ; underlined nucleotides match the experimentally determined consensus sequence shown in Fig. 2C.

f

Secondary metabolic cluster genes for calcium-dependent antibiotic.

g

Secondary metabolic cluster genes for actinorhodin.

h

Secondary metabolic cluster genes for undecylprodigiosin.

i

Secondary metabolic cluster genes for cryptic polyketide.

j

FAD, flavin adenine dinucleotide.