Table 2

High- and low-affinity cre boxes of the first genes of operons
Gene expression fold changea
Gene Strand cresequence Low CcpA induction Medium CcpA induction High CcpA induction crebox to TSS distanceb
High affinity cre boxes
1 acoR upper TGAAAGCGCTTTAT −4.8 −18.7 −21.7 −27
2 acsA lower TGAAAGCGTTACCA −2.3 −2.5 −2.7 +44
3 acuA upper TGAAAACGCTTTAT −2.2 −4.6 −7.7 −26
4 amyE upper TGTAAGCGTTAACA −2.6 −10.7 −12.9 +4
5 bglP lower TGAAAGCGTTGACA −2.5 −4.7 −4.6 −36
6 cccA lower TGTAAGCGTATACA −2.2 −1.8 −2.8 −29
7 citM upper TGTAAGCGGATTCA −2.6 −2.7 −2.9 +46
8 cstA lower TGAATGCGGTTACA −2.2 −1.9 −2.4 +32
9 dctP upper TGAAAACGCTATCA −7.4 −12.3 −16.6 −14
10 glpF upper TGACACCGCTTTCA −4.3 −21.9 −35.6 −27
11 gmuB upper TGTAAGCGTTTTAA −3.0 −15.6 −35.8 +6
12 iolA-1 lower TGAAAGCGTTTAAT −1.8 −1.9 −2.1 +93
13 iolA-2 (within iolB) lower TGAAAACGTTGTCA −2.2 −2.5 −2.4 +2404
14 manR upper TGTAAACGGTTTCT −2.0 −3.7 −8.0 0
15 msmX lower AGAAAGCGTTTACA −2.0 −2.6 −3.1 −15
16 rbsR upper TGTAAACGGTTACA −6.7 −15.2 −23.1 +6
17 rocG lower TTAAAGCGCTTACA −2.6 −3.5 −3.1 +43
18 sacP lower CGAAAACGCTATCA −2.1 −7.9 −8.1 −19
19 sucC upper TGAAAGCGCAGTCT −2.0 −5.8 −3.4 0
20 treP upper TGAAAACGCTTGCA −3.2 −13.0 −17.5 +372
21 uxaC upper TGAAAGCGTTATCA −2.5 −3.7 −8.9 +1237
22 xsa lower TAAAAGCGCTTACA −1.9 −1.8 −2.6 +7
23 xylA upper TGGAAGCGCAAACA −2.4 −11.9 −11.1 +144
24 xynP upper TGAAAGCGCTTTTA −4.0 −11.0 −17.9 +230
25 yisS upper AGAAAACGCTTTCT −1.9 −3.5 −3.7 +74
26 yjmD upper TGAAAGCGGTTCAA −2.2 −2.4 −8.8 ND
27 ykoM upper TGCAAGGGCTTTCA −2.0 −3.4 −3.5 +150
28 yrpD upper TGATAGCGTTTTCT −1.9 −8.0 −6.8 +127
29 ytkA lower TGTAAGCGTTTGCT −1.9 −6.4 −6.8 ND
30 yulD lower TGAAAGCGCTATCT −2.3 −4.9 −5.3 ND
31 yvfK lower TTAAAGCGCTTTCA −4.0 −6.1 −10.6 +5
Low affinity cre boxes
1 abnA lower TGTAAGCGCTTTCT −1.8 −1.7 −2.5 +85
2 acoA lower TGTAAGCGTTTGCT −1.1 −1.0 −1.8 +462
3 citZ lower TGTAAGCATTTTCT −1.5 −1.8 −2.1 +88
4 csbX lower TGAAAACGGTGCCA −1.4 −2.8 −2.1 −401
5 cydA lower TGAAATGAATCGTT 1.6 1.0 −2.7 −21
6 drm lower TGAAAACGGTTTAT −1.3 −3.6 −3.2 −16
7 gntR-1 upper TGAAAGTGTTTGCA −1.3 −2.8 −3.2 −41
8 gntR-2 upper TGAAAGCGGTACCA −1.3 −2.8 −3.2 +148
9 hutP upper TGAAACCGCTTCCA −1.3 −1.9 −2.6 +209
10 lcfA lower TGAAAACGTTATCA −1.4 −2.6 −2.6 +450
11 levD lower TGAAAACGCTTAAC −1.5 −1.2 −2.2 −45
12 malA upper TGTAAACGTTATCA −1.7 −2.0 −2.6 +6
13 mleN lower TGAAAGCGTTTTAG −1.5 −3.5 −2.4 +21
14 msmR upper TGTAACCGCTTACT −1.7 −4.2 −12.2 −28
15 mtlR upper TGAAAGCGTTTTAT −1.5 −2.7 −2.5 −16
16 odhA lower TGGAAGCGTTTTTA −1.6 −6.6 −3.4 +21
17 pbuG upper TGAAAACGTTTTTT −1.1 −1.5 −1.9 +245
18 pta lower TGAAAGCGCTATAA 1.3 −3.2 −2.7 −55
19 resA lower TAAAAACGCTTTCT −1.1 −1.9 −1.9 −72
20 sigL lower GGAAAACGCTTTCA −1.1 −3.1 −3.3 ND
21 wprA upper TGTAAGCGGTATCT −1.6 −5.5 −4.2 +43
22 yckB lower TGAAAACGCGATCA −1.4 −3.5 −2.1 −48
23 ycsA upper AGAAAGCGCTTACG −1.7 −6.0 −10.3 +67
24 ydzA lower TGAAAACGTGTCCA −1.3 −6.4 −6.4 +9
25 yesL upper TGAAAGCGTTTTCC −1.3 −1.6 −2.0 +125
26 yfiG upper AGAAAGCGGTTACA −1.6 −2.7 −4.6 +38
27 yncC upper TGTAAACGGTTACA −1.3 −2.4 −3.8 +84
28 yojA lower TGAAAGCGCTTTCT 1.1 −1.5 −1.8 +57
29 yqgW upper TGAAAACGCTATCG −1.1 −4.5 −4.2 −39
30 yqgY upper TGAAAATGTTTACA −1.4 −5.4 −4.1 −38
31 ysbA lower TGTAAGCGCTTTAT 1.0 −3.8 −7.6 ND
32 ysfC upper TGAAAGCGTTTTTT −1.5 −1.5 −2.0 +196
33 yugN lower TGAATGCGCTTTCT −1.7 −2.4 −2.3 ND
34 yuxG lower TGAAAACGGATACA −1.2 −4.2 −6.1 0
35 yvdG lower TGTAACCGCTTTCT −1.4 −1.5 −2.1 −28
36 yxlH upper TTGAAACGCTTTCA −1.4 −2.0 −2.3 +260
37 yydK upper TGTAAGCGGTTTAT −1.5 −3.2 −2.4 −21
38 yyzE lower TGAAAGCGTAACCA −1.2 −3.0 −2.1 0
Activating cre boxes
1 ilvB lower TGAAAGCGTATACA 3.0 6.2 2.7 +88
2 opuE lower TGAAAGCGTTTTAT 2.3 2.5 2.3 −103
3 ycbP lower TGAAAGCGCTCGCT 2.5 3.3 2.6 +30

a In bold – genes significantly regulated (1.8 < fold < −1.8).

bcre box distance to transcriptional start site calculated from the conserved G residue in the middle CpG of the cre box.

Marciniak et al.

Marciniak et al. BMC Genomics 2012 13:401   doi:10.1186/1471-2164-13-401

Open Data