Table 1 Results of ChAP-Seq analysis with C. glutamicum ATCC13032ΔftsR/pAN6-ftsR-Strep. The nine DNA regions that showed a ≥ 50-fold higher coverage than the entire genome (coverage 40) in the ChAP-Seq analysis with FtsR-Strep were analyzed with respect to the location of the peak within the genome and the mRNA levels of the genes in this region. Based on that, a prediction was made which genes could be potential FtsR targets. The arrows indicate whether the genes are encoded on the leading (→) or lagging strand (←) within the genome. Graphical representations of selected peaks as derived from the ChAP-Seq analysis are shown in Additional file 1: Figure S10

in gene

downstream 3′-end of

upstream of

Gene

mRNA ratio

p-value

1 (1)

28,811 (4781)

–

cg2478 (NCgl2178, penicillin binding protein) ←

cg2477 (NCgl2177, conserved hypothetical protein) ←

cg2478

0.75

0.11

cg2477 potentially activated by FtsR

cg2477

0.24

0.01

2 (5)

22,757 (934)

–

–

cg3182 (NCgl2777, cop1, trehalose corynemycolyl transferase) ←

cg3182

1.70

0.20

cop1-cg3181-cg3180 potentially repressed by FtsR

cg3181

2.30

0.05

cg3180

1.91

0.05

cg3181 (NCgl2776, put. Secreted protein) ←

cg3180 (NCgl2775, put. Secreted protein) ←

cg3183 (NCgl2778, put. transposase) →

cg3183

n.a.

n.a.

3 (2)

4437 (1556)

–

cg2367 (NCgl2076, ftsQ, cell division septal protein) ←

cg2366 (NCgl2075, ftsZ, cell division GTPase) ←

cg2367

1.20

0.02

ftsZ activated by FtsR

cg2366

0.35

0.02

4 (11)

3899 (373)

cg0470 (NCgl0381, htaB, heme transport-associated protein) →

cg0469 (NCgl0380, hmuV) →

cg0471 (NCgl0382, htaC, heme-transport associated protein) →

cg0469

1.41

< 0.01

–

cg0470

1.45

0.09

cg0471

1.55

0.03

5 (12)

3836 (365)

–

–

cg0852 (NCgl0712, conserv. Hypoth. protein) ←

cg0852

0.62

0.01

cg0852 potentially activated by FtsR

cg0853 (NCgl0713, conserv. Hypoth. protein) →

cg0854 (NCgl0714, pmmA, phosphomannomutase) →

cg0855 (NCgl0715, conserv. Hypoth. protein) →

cg0856 (NCgl0716, mannose-6-phosphate isomerase) →

cg0853

1.03

0.29

cg0854

0.89

0.25

cg0855

1.18

0.08

cg0856

1.09

0.03

6 (3)

3630 (1529)

–

cg3392 (oxiE, idhA2, NCgl2958) →

(myo-inositol 2-dehydrogenase)

cg3393 (NCgl2959, phoC, secreted cell-wall-associated phosphatase) →

cg3392

1.25

0.03

phoC potentially repressed by FtsR

cg3393

1.60

0.03

7 (15)

2871 (315)

cg2695 (NCgl2368, ATPase of ABC transporter) ←

cg2697 (ssb, NCgl2370, single-strand DNA-binding protein) ←

cg2694 (NCgl2367, put. Phosphodiesterase, nucleotide pyrophosphatase) ←

cg2693 (NCgl2366, put. Phosphodiesterase, nucleotide pyrophosphatase) ←

cg2693

1.31

0.03

–

cg2694

1.29

0.05

cg2695

1.06

0.42

cg2697

1.04

0.24

8 (6)

2355 (858)

–

cg2518 (NCgl2213, put. Secreted protein) →

cg2519 (NCgl2214, conserv. Hypoth. protein) ←

cg2520 (NCgl2215, hypoth. protein) ←

cg2521 (NCgl2216, fadD15, long chain fatty acid CoA ligase) ←

–

cg2518

0.81

0.18

–

cg2519

0.49

0.03

cg2520

0.92

0.45

cg2521

0.91

0.43

9 (8)

2248

cg0839 (NCgl0701) ← (hypoth. protein)

cg0840 (NCgl0702, conserv. Hypoth. protein) ←

cg0838 (NCgl0700, ATP-depend. helicase) ←

cg0838

4.61

0.03

cg0838 potentially repressed

cg0839

2.45

0.16

by FtsR

cg0840

2.45

0.19