High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis

Marciniak, Bogumiła C; Pabijaniak, Monika; de Jong, Anne; Dűhring, Robert; Seidel, Gerald; Hillen, Wolfgang; Kuipers, Oscar P

doi:10.1186/1471-2164-13-401

BMC Genomics

Table 2 High- and low-affinity cre boxes of the first genes of operons

From: High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis

				Gene expression fold change^a
	Gene	Strand	cresequence	Low CcpA induction	Medium CcpA induction	High CcpA induction	*cre*box to TSS distance^b
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.

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