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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

AccessionGene DescriptionLog2FCbMeanc
Histidine
EAMY_1255hutH, histidine ammonia-lyase6.978.62
EAMY_1254hutU, urocanate hydratase5.88.85
EAMY_1259hutI, imidazolonepropionase4.934.93
EAMY_1258hutF, formiminoglutamate deiminase4.756.60
EAMY_1260hutG, N-formylglutamate amidohydrolase3.26.31
EAMY_1256hutC, transcriptional regulator1.096.71
Methionine
EAMY_0207metR, transcriptional regulator5.479.21
EAMY_0208metE, methionine synthase II4.8613.30
EAMY_0141metF, 5,10-methylenetetrahydrofolate reductase4.7110.82
EAMY_0138metB, cystathionine gamma-synthase4.5610.43
EAMY_0603metK, S-adenosylmethionine synthetase4.3211.75
EAMY_3342metA, homoserine transsuccinylase3.49.95
EAMY_0139metL, bifunctional aspartokinase3.3110.48
EAMY_0137metJ, transcriptional regulator of met regulon2.418.53
Arginine
EAMY_1553argC, acetylglutamate semialdehyde dehydrogenase2.4111.13
EAMY_0144argB, acetylglutamate kinase2.1710.74
EAMY_0297argR, arginine repressor1.938.35
EAMY_0146argH, argininosuccinate lyase1.8810.84
EAMY_0145argG, argininosuccinate synthase1.8311.69
EAMY_3415argD, 4-aminobutyrate aminotransferase1.8310.43
EAMY_2082argS, arginyl-tRNA synthetase1.378.58
EAMY_1631astB, succinylarginine dihydrolase−3.056.66
EAMY_1630astD, NAD-dependent aldehyde dehydrogenase−1.986.45
EAMY_1628astC, succinylornithine transaminase−1.887.19
EAMY_1629astA, arginine N-succinyltransferase−1.606.15
Tryptophan
EAMY_1915trpE, anthranilate synthase component I3.6711.22
EAMY_1916trpG, anthranilate synthase component II2.738.92
EAMY_1917trpD, anthranilate phosphoribosyltransferase2.49.21
EAMY_1918trpC, indole-3-glycerol phosphate synthase1.829.45
EAMY_1919trpB, tryptophan synthase beta chain1.499.28
EAMY_3425trpS, tryptophanyl-tRNA synthetase1.318.67
Isoleucine
EAMY_0158ilvG, acetolactate synthase isozyme III large subunit3.6010.64
EAMY_0159ilvM, acetolactate synthase isozyme II small subunit2.698.25
EAMY_0160ilvE, branched-chain amino acidaminotransferase2.179.33
EAMY_0161ilvD, dihydroxy-acid dehydratase1.219.57
EAMY_0163ilvY, transcriptional regulator1.125.24
  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