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Table 1 GlnR binding regions identified by ChIP-seq and corresponding gene expression fold change (wild type vs glnR deletion strain) in M. smegmatis during nitrogen limitation

From: Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

Peak no.a

Coordinatesb

Peak intensityc

Adjacent gene (s)d

Fold change in gene expressione

Gene annotation

1

501431-501471

8.4

MSMEG0427*

76.4

nirB Nitrite reductase, large subunit

2

508651-508691

42.9

MSMEG0432*

18.3

nnaR Transcriptional regulator

3

510091-510131

8.4

MSMEG0433

24.6

narK3 Nitrate extrusion protein

4

647871-647911

27.1

MSMEG0572*

263.4

Putative uncharacterised protein

5

864391-864431

6.1

MSMEG0780L*

23.0

Phosphotransferase enzyme family protein

   

MSMEG0781R

8.4

Amino acid permease

6

1121631-1121671

54.3

MSMEG1052

6.3

Amino acid carrier protein

7

1142851-1142891

6.5

MSMEG1078L

-3.8

Hydrolase

   

MSMEG1079R*

3.4

Putative uncharacterised protein

8

1146711-1146751

71.9

MSMEG1082

277.4

Putative response regulator, LuxR family

9

1238491-1238531

19.3

MSMEG1177L

10.7

Cytosine/purines/uracil/thiamine/allantoin permease

   

MSMEG1178R

3.5

Transcriptional regulator

10

1385631-1385671

6.48

MSMEG1292L*

2.4

Dehydrogenase protein

   

MSMEG1293R*

4.2

Xanthine/uracil permeases family protein

11

1684231-1684271

64.6

MSMEG1597

2.8

Transcription factor WhiB

12

1832291-1832331

46.5

MSMEG1738

-13.2

Probable conserved transmembrane protein

13

1965171-1965211

19.3

MSMEG1886

No DE

Fatty acid desaturase

14

2000471-2000511

10.9

MSMEG1919

No DE

Transcription factor WhiB

15

2070111-2070151

9.9

MSMEG1987*

120.7

Putative uncharacterised protein

16

2081471-2081511

19.5

MSMEG1999

-2.1

Putative uncharacterised protein

17

2260871-2260911

39.9

MSMEG2183L

2.3

Conserved hypothetical protein

   

MSMEG2184R*

38.8

Amino acid permease

18

2414891-2414931

67.9

MSMEG2332

10.1g

Amino acid carrier protein

19

2508191-2508231

101.5

MSMEG2425*

98.8

amtB Ammonium transporter

20

2592931-2592971

18.6

MSMEG2506*

-4.1

Carboxyvinyl-carboxyphosphonate phosphorylmutase

21

2608351-2608391

171.1

MSMEG2522*

165.9

Efflux ABC transporter, permease protein

22

2612531-2612571

331.2

MSMEG2526

782.4

Copper amine oxidase

23

2655531-2655571

56.3

MSMEG2570*

50.8

Xanthine/uracil permease

24

3048291-3048331

105.9

MSMEG2982*

583.8

Putative periplasmic binding protein

25

3206851-3206891

8.7

MSMEG3131L

-1.44

Polypeptide: AMP-binding protein

   

MSMEG3132R

No DE

Polypeptide: DNA-binding protein

26

3237471-3237511

6.5

MSMEG3166

No DE

Enzyme: beta-lactamase

27

3471571-3471611

8.2

MSMEG3400*

228.0

Glutamyl-tRNA(Gln) amidotransferase subunit A

28

4043191-4043231

22.8

MSMEG3975

2.1

Putative regulatory protein, PucR family

29

4069251-4069291

58.9

MSMEG3995

9.7

N-carbomoyl-L-amino acid amidohydrolase

30

4070051-4070091

13.2

MSMEG3996L

8.3

hydA Dihydropyrimidinase

   

MSMEG3997R

6.5

Regulatory protein, PucR family

31

4082411-4082451

77.2

MSMEG4008*

49.2

Oxidoreductase, 2OG-Fe(II) oxygenase family protein

32

4136531-4136571

7.4

MSMEG4063

No DE

Polypeptide: amidohydrolase

33

4290471-4290511

8.0

MSMEG4206

115.7

Molybdopterin oxidoreductase

34

4374791-4374831

184.7

MSMEG4290

20.0

glnA Glutamine synthetase

35

4381891-4381931

49.8

MSMEG4294

12.6

glnA Glutamine synthetase, type I

36

4580191-4580231

384.4

MSMEG4501

103.3

Sodium:dicarboxylate symporter

37

4722511-4722551

17.1

MSMEG4635*

102.0

amtA Ammonium transporter

38

4726751-4726791

63.6

MSMEG4639*

57.3

Putative uncharacterised protein

39

4729431-4729471

11.1

MSMEG4643

No DE

Resuscitation-promoting factor

40

4729931-4729971

34.4

MSMEG4643

No DE

Resuscitation-promoting factor

41

5183411-5183451

57.5

MSMEG5084*

27.1

Glycosyl transferase, group 2 family protein

42

5440611-5440651

233.9

MSMEG5358

14.9

Acetamidase/Formamidase family protein

43

5442051-5442091

27.2

MSMEG5360*

29.1

Formate/nitrate transporter

44

5651011-5651051

18.6

MSMEG5561

1.40

HPP family protein

45

5840591-5840631

11.6

MSMEG5765

4.1

glbN Globin

46

6177591-6177631

31.6

MSMEG6116

24.8

Putative allantoicase

47

6323551-6323591

23.7

MSMEG6259

255.9

amt1 Ammonium transporter

48

6714291-6714331

16.3

MSMEG6660

8.1

Cytosine/purine/uracil/thiamine/allantoin permease

49

6747051-6747091

9.9

MSMEG6695L

No DE

Cytochrome P450

   

MSMEG6697R

No DE

IS1096, tnpA protein

50

6782771-6782811

17.7

MSMEG6735*

128.3

Amino acid permease, putative

51

6865371-6865411

199.7

MSMEG6816

385.3

Molybdopterin oxidoreductase

52

6867931-6867971

12.7

N/A

N/A

N/A

53

6930751-6930791

10.8

MSMEG6881

5.8

Transcriptional regulator, GntR family

  1. aassigned peak number, bpeak coordinates on the M. smegmatis genome, cfold enrichment of each peak compared to the input control calculated using SISSRs, dadjacent gene(s) to peak, efold change in gene expression (WT vs ΔglnR) and gfold change in gene expression normalized to sigA from qRT-PCR (WT vs ΔglnR). L = left and R = right indicates the direction of the gene in relation to GlnR binding where GlnR is proposed to control divergent genes. Genes in operons are denoted by *. Peaks that represent binding sites with no corresponding differential expression of adjacent genes are labelled no DE.
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BMC Genomics

ISSN: 1471-2164

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