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Table 4 List of differentially expressed genesa associated with amino acid biosynthesis and degradation for the (p) ppGpp0 mutant versus WT at 3 h

From: The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora

Accession

Gene Description

Log2FCb

Meanc

Histidine

 EAMY_1255

hutH, histidine ammonia-lyase

6.97

8.62

 EAMY_1254

hutU, urocanate hydratase

5.8

8.85

 EAMY_1259

hutI, imidazolonepropionase

4.93

4.93

 EAMY_1258

hutF, formiminoglutamate deiminase

4.75

6.60

 EAMY_1260

hutG, N-formylglutamate amidohydrolase

3.2

6.31

 EAMY_1256

hutC, transcriptional regulator

1.09

6.71

Methionine

 EAMY_0207

metR, transcriptional regulator

5.47

9.21

 EAMY_0208

metE, methionine synthase II

4.86

13.30

 EAMY_0141

metF, 5,10-methylenetetrahydrofolate reductase

4.71

10.82

 EAMY_0138

metB, cystathionine gamma-synthase

4.56

10.43

 EAMY_0603

metK, S-adenosylmethionine synthetase

4.32

11.75

 EAMY_3342

metA, homoserine transsuccinylase

3.4

9.95

 EAMY_0139

metL, bifunctional aspartokinase

3.31

10.48

 EAMY_0137

metJ, transcriptional regulator of met regulon

2.41

8.53

Arginine

 EAMY_1553

argC, acetylglutamate semialdehyde dehydrogenase

2.41

11.13

 EAMY_0144

argB, acetylglutamate kinase

2.17

10.74

 EAMY_0297

argR, arginine repressor

1.93

8.35

 EAMY_0146

argH, argininosuccinate lyase

1.88

10.84

 EAMY_0145

argG, argininosuccinate synthase

1.83

11.69

 EAMY_3415

argD, 4-aminobutyrate aminotransferase

1.83

10.43

 EAMY_2082

argS, arginyl-tRNA synthetase

1.37

8.58

 EAMY_1631

astB, succinylarginine dihydrolase

−3.05

6.66

 EAMY_1630

astD, NAD-dependent aldehyde dehydrogenase

−1.98

6.45

 EAMY_1628

astC, succinylornithine transaminase

−1.88

7.19

 EAMY_1629

astA, arginine N-succinyltransferase

−1.60

6.15

Tryptophan

 EAMY_1915

trpE, anthranilate synthase component I

3.67

11.22

 EAMY_1916

trpG, anthranilate synthase component II

2.73

8.92

 EAMY_1917

trpD, anthranilate phosphoribosyltransferase

2.4

9.21

 EAMY_1918

trpC, indole-3-glycerol phosphate synthase

1.82

9.45

 EAMY_1919

trpB, tryptophan synthase beta chain

1.49

9.28

 EAMY_3425

trpS, tryptophanyl-tRNA synthetase

1.31

8.67

Isoleucine

 EAMY_0158

ilvG, acetolactate synthase isozyme III large subunit

3.60

10.64

 EAMY_0159

ilvM, acetolactate synthase isozyme II small subunit

2.69

8.25

 EAMY_0160

ilvE, branched-chain amino acidaminotransferase

2.17

9.33

 EAMY_0161

ilvD, dihydroxy-acid dehydratase

1.21

9.57

 EAMY_0163

ilvY, transcriptional regulator

1.12

5.24

  1. aDifferentially expressed genes (DEGs) between the (p) ppGpp0 mutant and WT at 3 h with |log2FC| value ≥ 1 and an adjusted p value < 0.05. WT: wild type. FC: fold change. FC values below 0 mean that the gene has lower expression in the (p) ppGpp0 mutant than in WT, and vice versa
  2. blog2FC valus was calculated by the log based 2 value of (p) ppGpp0 / WT at 3 h
  3. cThe average of log2CPM was calculated. CPM: count per million reads
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BMC Genomics

ISSN: 1471-2164

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