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Table 1 Genes directly regulated by CodY in S. salivarius 57.I

From: Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius

Function category/

Locus_tag

Gene/

Homologa

ΔcodY/57.Ib

Position(nt)c

Predicated CodY binding sequence

Noted

20 mM Glu

100 mM Glu

pH 7

pH 5.5

pH 7

pH 5.5

Peptide uptake and degradation

 Ssal_00190

oppA

ns

ns

1.5

ns

94

AATATTCAGAAAGTA

 

 Ssal_00280

pepP

ns

4.3

ns

1.3

39

TAAAGTCTGAAAATT

 

 Ssal_01946

pepC

3.3

ns

ns

ns

42

AATTTTCAGAAATTA

 

Amino acid uptake and biosynthesis

 Ssal_00127

thrC

1.6

ns

2.9

1.45

43

AATATTCTGACAATT

 

 Ssal_00131

ilvD

3.2

7.7

ns

3.1

66

AATATTCTGAAAATT

 

 Ssal_00132

ilvB

3.6

4.0

88.1

5.1

30

AATTTTTAGACAATT

Ssal_00132–00134 are predicted to be an operon

 Ssal_00133

ilvH

5.1

6.3

4.4

2.4

  

 Ssal_00134

ilvC

5.3

9.7

2.4

1.6

  

 Ssal_00456

–

5.4

ns

ns

1.6

336

AATTAACAGAAAATT

Ssal_00456–00465 are predicted to be an operon

 Ssal_00457

trpE

1.5

2.5

ns

1.6

  

 Ssal_00458

trpG

ns

3.5

ns

ns

  

 Ssal_00459

trpD

ns

2.3

ns

1.6

  

 Ssal_00461

trpC

ns

2.4

ns

ns

  

 Ssal_00462

trpF

ns

2.1

ns

ns

  

 Ssal_00464

trpB

ns

2.7

ns

ns

  

 Ssal_00465

trpA

ns

2.2

ns

1.5

  

 Ssal_00537

serC

2.0

2.6

2.5

2.6

38

AATATTCAGAAAATT

Ssal_00537–00539 are a predicted to be an operon

 Ssal_00538

–

1.5

5.0

2.3

1.7

  

 Ssal_00539

serA

3.1

6.5

1.7

2.6

  

 Ssal_00884

dapA

1.8

ns

1.6

ns

74

CGTTTTCAGAAAATT

 

 Ssal_00898

pdxU2

2.6

3.3

2.8

3.8

41

AATCGTCAGAATTTT

Ssal_00898–00900 are predicted to be an operon

 Ssal_00899

pdxK

4.6

4.6

2.8

3.3

  

 Ssal_00900

pdxU

3.9

2.6

4.3

3.1

  

 Ssal_01037

ilvB

3.6

5.3

1.8

ns

154

AAAATTCACAATCTT

 

129

GATTGTCTGAAAACT

 Ssal_01272

leuD

1.8

ns

ns

ns

  

Ssal_01276–01272 are predicted to be an operon

 Ssal_01273

leuC

2.4

3.1

2.2

ns

  

 Ssal_01275

leuB

2.8

2.8

20.5

ns

  

 Ssal_01276

leuA

3.1

4.4

1.8

ns

242

AAAAGTCAGTCAATT

 Ssal_01351

mprF

1.8

2.9

3.5

1.6

  

Ssal_01352–01351 are predicted to be an operon

 Ssal_01352

–

ns

2.7

23.2

ns

134

AATATTCTGACTCTT

 Ssal_01567

ilvE

5.8

3.6

11.1

4.2

75

AATTGTCAGAATTTT

 

 Ssal_01655

pheP

5.1

2.3

2.2

4.0

95

AAAATTCTGAATATT

 

 Ssal_01693

thrB

2.5

ns

ns

1.7

  

Ssal_01694–01693 are predicted to be an operon

 Ssal_01694

–

1.8

1.8

ns

ns

98

AATTTTCAGTAAAAA

55

AATATTCTGTCAATT

 Ssal_01811

lysC

5.9

5.2

9.4

5.6

39

AATTGTCAGAATTTT

 

 Ssal_01812

asnA

3.3

2.1

ns

1.7

61

AATTGTTGGAAAATT

 

41

ATTTTTCTGAAAAAT

 Ssal_01828

livF

1.7

4.3

2.2

1.7

  

Ssal_01832–01828 are predicted to be an operon

 Ssal_01829

livG

1.5

6.7

4.3

1.8

  

 Ssal_01830

livM

ns

3.5

36.1

1.3

  

 Ssal_01831

livH

ns

9.2

3.4

2.6

  

 Ssal_01832

livK

ns

12.5

5.5

2.0

192

ACTATTCTGATATTG

14

AATTGTCTGATAATT

 Ssal_01840

metB

ns

ns

5.0

ns

215

ATGTTTCAGGCACTT

 

62

TATTTTCAGAAAATA

 Ssal_02023

ilvA

3.1

3.3

ns

1.7

45

TTTTTTCTGAAAATT

 
      

17

AATAGTTTGAATATT

 

Urease operon

 Ssal_01891

ureO

8.0

8.3

2.3

ns

  

Ssal_01903–01891 are predicted to be an operon

Ssal_01903 and Ssal_01904 are in opposite orientations

 Ssal_01892

ureQ

3.5

5.0

2.4

1.8

  

 Ssal_01894

ureM

2.0

3.3

2.2

1.6

  

 Ssal_01895

ureD

ns

6.3

1.7

ns

  

 Ssal_01896

ureG

ns

3.5

4.6

ns

  

 Ssal_01897

ureF

ns

4.3

2.0

ns

  

 Ssal_01898

ureE

ns

3.8

2.9

1.2

  

 Ssal_01900

ureC

4.1

2.5

ns

2.6

  

 Ssal_01901

ureB

ns

ns

1.9

ns

  

 Ssal_01902

ureA

ns

2.8

1.8

ns

  

 Ssal_01903

ureI

2.0

3.5

2.2

1.6

211

TATTGTCAGAAACAG

58

AAATTTCTGAAAATT

 Ssal_01904

–

6.1

2.0

12.2

4.3

334

AATTTTCAGAAATTT

 
      

181

CTGTTTCTGACAATA

 

Other transporters

 

 Ssal_00845

–

2.5

2.0

57.1

13.8

69

TAATTTCAGAAAATT

 

 Ssal_00908

–

33.9

16.7

55.1

16.6

92

ATTTTTCAGAAAATA

 

60

ATTATTCCAACAATT

19

ATTATTCTGAAAATT

 Ssal_01154

–

ns

2.8

7.8

1.3

144

AATATTCGGAAAATA

 

 Ssal_01464

–

7.1

7.1

7.1

2.4

  

Ssal_01466–01464 are predicted to be an operon

 Ssal_01465

fhuC

4.9

7.1

2.7

2.5

  

 Ssal_01466

hmuU

8.7

7.9

3.9

4.7

116

AATTTTCTGACATTA

Regulation

 Ssal_00404

codY

nd

nd

nd

nd

116

AATTTTCAGACAATT

 

 Ssal_00555

cidA

2.2

ns

2.1

1.4

175

AAATATTTGACTATT

Ssal_00555–00556 are predicted to be an operon

79

AATTTACTGAAAACT

 Ssal_00556

cidB

1.6

ns

3.2

1.7

  

 Ssal_00962

–

21.8

18.6

21.9

19.8

108

AAGTATCTGAAATAG

 

39

AATTTTCAGAATATT

 Ssal_01667

glnB

43.2

8.4

3.4

6.0

  

Ssal_01668–01667 are predicted to be an operon

 Ssal_01668

nrgA

15.2

19.9

61.2

7.5

361

CTATTTCAGAAGTTT

292

GAGCTTCTGAAAATG

78

AATTATCAAAAAATT

 Ssal_01704

–

2.5

ns

9.1

2.1

10

AATTATCAGAAAAGG

 

 Ssal_01769

nadR

ns

ns

4.9

1.4

288

AATTTTCAGAATCTT

 

264

TATTTTCTGCTATTT

Carbon metabolism

 Ssal_01359

–

2.4

3.1

4.1

3.4

  

Ssal_01360–01359 are predicted to be an operon

 Ssal_01360

gapN

3.4

6.3

ns

1.5

74

AATTTTCTGAATAAT

 Ssal_01545

–

4.7

2.7

3.3

3.1

  

Ssal_01546–01545 are predicted to be an operon

 Ssal_01546

folD

3.8

4.9

3.0

3.2

138

CATAATCAGAAAAAA

72

AAAATTTAGAAAATT

 Ssal_01768

gdhA

12.9

15.7

3.5

6.3

353

GCTTTCCTGATAATT

 

61

AAATAGCAGAAAATA

 Ssal_01810

pgmB

ns

ns

3.6

ns

75

AAAATTCTGACAATT

 

Others

 Ssal_00112

–

3.5

2.3

4.4

1.4

44

AATCGTCTGAATATT

 

 Ssal_00214

–

ns

ns

ns

2.1

324

CATCTTCTGAAATTT

 

 Ssal_00216

–

3.3

2.1

2.8

ns

229

AAATTTCAGAAGATG

 

 Ssal_00672

–

72.1

247.7

73.6

41.8

178

AATTGTCAGACAACT

 

123

AATTGTCAGAATGTT

 Ssal_00714

–

ns

7.3

2.2

ns

108

ACTTTTCTAAAAATT

 

 Ssal_01153

udg

1.9

ns

ns

4.1

129

TATTTTCCGAATATT

 

 Ssal_01428

lysM

ns

3.9

ns

8.7

143

AAATGTCAGATAAAT

 

 Ssal_01429

lysS

ns

3.2

ns

1.215

69

ATTTATCTGACATTT

 
  1. a, −, no assigned gene name
  2. b, The values are the RPKM of the locus in S. salivarius ΔcodY divided by that in wild-type 57.I under the same growth condition. ns, no significant difference. nd, not determined
  3. c, The distance (in nucleotides) of the predicted CodY binding consensus to the translation start site of the locus
  4. d, Operons started with a lower tag number are transcribed from the minus strand
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