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Table 2 PhaR-repressed genes associated with a PhaR-binding consensus sequence

From: Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation

Gene or orf

PhaR binding site

USDA110 RPKM

ΔphaR RPKM

Fold changea

Description

cyoA (blr0149)

TGCGGCGCAGCA

22.29

77.7

3.49

cytochrome O ubiquinol oxidase subunit II

phaZ3 (blr0899)

TGCAGTGCAGCA

32.68

89.48

2.74

poly(3-hydroxyalkanoate) depolymerase

phaZ1 (blr0908)

CGCATCGCAGCA

129.32

542.25

4.19

poly(3-hydroxybutyrate) depolymerase

rhlE (bll1447)

TGCAGTGCAGAA

152.94

551.69

3.61

dead-box ATP-dependent RNA helicas

blr2242

TGCGCCGCAGCA

66.21

190.65

2.88

unknown protein

bll2363

TGCGCCGCACAA

374.44

1256.32

3.36

unknown protein

blr2367

TGCACCGCAGCA

55.14

347.34

6.30

acetyltransferase

bll2471

TGGATCGCACCA

86.78

512.16

5.90

hypothetical protein (Hemerythrin HHE cation binding region)

bll2537

CGCGTCGCAGCA

39.54

83.05

2.10

hypothetical protein

phaP5 (blr2887)

TGCATCGCACAA

122.86

15,882.63

129.27

phasin

ppc (blr2955)

TGCGCTGCGGCA

46.27

93.71

2.03

PEP carboxylase

bll3794

TGCATTGCAGCG

104.59

404.72

3.87

hypothetical protein

blr4162

TGCATCGCACCA

79.46

931

11.72

hypothetical protein (cellulose synthase catalytic subunit protein)

bsr4236

TGCATTGCAACA

38.73

435.02

11.23

unknown protein

nifR (blr4486)

TGCAGTGCAGCA

112.16

225.25

2.01

nitrogen regulation protein

metN (blr4501)

TGCACCGCAACA

14.42

29.08

2.02

probable ABC transporter ATP-binding protein

bsr4726

TGCGGTGCACAC

157.38

1402.14

8.91

hypothetical protein

bll4785

CGCGCCGCACAA

90.88

279.72

3.08

transcriptional regulatory protein Fis family

phaP1 (bll5155)

TGCAACGCACAA

215.67

10,738.12

49.79

phasin

bsr5273

TGCGGTGCATCA

45.13

222.49

4.93

hypothetical protein

bll5524

AGCAGTGCAGCA

106.54

220.06

2.07

hypothetical protein

blr5525

AGCAGTGCAGCA

23.4

46.85

2.00

hypothetical protein

blr5594

TGCGGCGCACAA

26.16

71.75

2.74

MFS permease

bll6290

TGCGGCGGACCA

146.99

458.11

3.12

two-component response regulator

blr6718

TGCCATGCAGCA

42.45

111.4

2.62

hypothetical protein

nirK (blr7089)

TGCGCTGCAACA

13.49

41.36

3.07

respiratory nitrite reductase

phaP4 (bll7395)

TGCGCTGCACAA

489.78

2956.78

6.04

phasin

blr7872

TGCGCTGCAACA

6.30

20.63

3.27

HlyD family secretion protein

  1. aFold change: ΔphaR RPKM/USDA110 RPKM