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Table 2 S. lividans TK24 genes with (partially) known function with expression correlating to that of the OsdR regulatory protein, and significantly higher expression in a CelA-producing strain in exponential phase (Benjamini–Hochberg FDR 0.05)

From: Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein

Locus

Function

Expression [TPM]

p-value

SLIV

SCO

Ref.

CelA

log2(FC)

01755

7511

Glyceraldehyde-3-phosphate dehydrogenase Gap3

52

323

2.65

2.8e−08

05195

6663

Transketolase

25

207

3.06

4.0e−13

05200

6662

Transaldolase 1

53

158

1.57

3.6e−04

05205

6661

Glucose-6-phosphate 1-dehydrogenase

40

110

1.46

1.9e−04

05215

6659

Glucose-6-phosphate isomerase 1

64

134

1.06

2.4e−03

05220

6658

6-phosphogluconate dehydrogenase

144

221

0.62

4.0e−02*

05225

6657

Membrane-associated oxidoreductase

26

33

0.32

3.9e−01*

18590

3946

CydB cytochrome d ubiquinol oxidase, subunit II

127

204

0.68

2.4e−02*

18595

3945

CydA cytochrome oxidase subunit I

250

892

1.83

2.0e−09

33310

0924

Cytochrome B subunit

45

273

2.59

5.9e−09

33315

0923

Fumarate dehydrogenase

17

96

2.50

3.9e−09

33320

0922

Fumarate dehydrogenase

26

78

1.59

3.1e−03

36805

0219

Respiratory nitrate reductase, gamma subunit

0

28

Inf

5.2e−07

36810

0218

Nitrate reductase subunit delta

0

36

Inf

2.0e−08

36815

0217

Nitrate reductase beta chain

0

111

8.23

1.0e−28

36820

0216

Nitrate reductase alpha subunit

2

192

6.86

3.5e−49

36825

0215

\(\hbox {Nitroreductase}^{\dagger }\)

1

82

7.14

4.0e−15

36830

0214

Pyridoxamine 5′-phosphate \(\hbox {oxidase}^{\dagger }\)

4

58

4.03

1.4e−04

36835

0213

Nitrate/nitrite transporter

3

114

5.46

1.0e−20

36845

0211

Two-component sensor

2

73

5.21

1.4e−08

36850

0209

Cystathionine \(\beta \)-\(\hbox {syntase}^{\dagger }\)

1

109

6.97

1.4e−20

36855

0208

Pyruvate, phosphate dikinase

1

65

5.90

5.4e−24

36865

0206

Putative pyruvate formate-lyase

0

74

Inf

3.1e−05

36867

 

Putative pyruvate formate-lyase-activating protein, N-terminal fragment, putative pseudogene

0

74

Inf

7.7e−06

36875

0204

Transcriptional regulatory protein OsdR

16

391

4.60

3.1e−25

36880

0203

Two-component sensor OsdK

23

56

1.30

4.2e−03*

36890

0201

Thiosulfate dehydrogenase (quinone)\(^{\dagger }\)

1

464

8.97

3.5e−37

36895

0200

Universal stress \(\hbox {protein}^{\dagger }\)

0

317

Inf

2.5e−04

36900

0199

Alcohol dehydrogenase

1

214

8.55

9.3e−26

36905

0198

Universal stress \(\hbox {protein}^{\dagger }\)

1

72

6.16

2.9e−11

36910

0197

Pyridoxamine 5′-phosphate \(\hbox {oxidase}^{\dagger }\)

6

97

4.07

3.1e−09

37035

0181

Universal stress \(\hbox {protein}^{\dagger }\)

2

175

6.76

4.0e−22

37040

0180

Universal stress \(\hbox {protein}^{\dagger }\)

0

69

Inf

2.7e−14

37045

0179

Zinc-containing dehydrogenase

4

293

6.37

6.9e−32

37050

0178

Universal stress \(\hbox {protein}^{\dagger }\)

8

28

1.72

1.2e−01

37060

0177

Membrane protein

2

112

6.22

2.5e−12

37070

0174

pyridoxamine 5′-phosphate \(\hbox {oxidase}^{\dagger }\)

1

232

8.50

6.0e−32

37075

0173

OsmC regulator of disulfide bond formation redox \(\hbox {protein}^{\dagger }\)

7

78

3.48

2.8e−06

37080

0172

Universal stress \(\hbox {protein}^{\dagger }\)

3

17

2.76

1.1e−01

37085

0171

Nicotinate phosphoribosyltransferase

0

56

Inf

3.5e−17

37095

0169

Cystathionine \(\beta \)-\(\hbox {synthase}^{\dagger }\)

10

398

5.29

4.0e−30

37100

0168

Regulator protein

10

625

5.94

5.1e−33

37105

0167

Universal stress \(\hbox {protein}^{\dagger }\)

4

297

6.35

8.5e−31

37130

0162

\(\hbox {Nitroreductase}^{\dagger }\)

0

91

8.28

3.5e−17

37090

0170

Cystathionine \(\beta \)-\(\hbox {synthase}^{\dagger }\)

6

252

5.44

1.2e−21

  1. A clustering algorithm was used for grouping nearby genes with similar expression patterns. When present, the corresponding ortholog of the model organism S. coelicolor is given
  2. * Genes included for completeness, but p-value does not satisfy FDR 0.05
  3. †Function taken from [42]