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Table 6 List of differentially expressed genesa associated with amino acid and peptide transport systems 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
amino acid transport system
  EAMY_2728metN, methionine ABC transporter ATP-binding protein3.249.03
  EAMY_2729metI, methionine ABC transport system1.317.53
Arginine (PAAT)
  EAMY_0862ABC-type arginine/histidine transport system, permease component2.243.66
  EAMY_1315artP, arginine ABC transport system1.679.20
  EAMY_1314artI, arginine ABC transport system1.339.86
Other polar amino acid uptake transport system (PAAT)
  EAMY_0860ABC transporter substrate-binding protein5.284.96
  EAMY_0266yhdW, ABC transporter substrate-binding protein3.476.70
  EAMY_0861polar amino acid ABC transporter permease3.364.07
  EAMY_0863ABC transporter ATP-binding protein2.524.44
  EAMY_0263yhdZ, ABC-type polar amino acid transport system1.424.52
  EAMY_0264yhdY, ABC-type amino acid transport system1.274.15
  EAMY_0265yhdX, ABC-type amino acid transport system1.124.63
peptide transport system
  EAMY_1936oppB, ABC transporter permease componenet−2.655.91
  EAMY_1935oppC, ABC transporter permease componenet−2.435.27
  EAMY_1937oppA, ABC transporter periplasmic component−2.299.25
  EAMY_1934oppD, ABC transporter ATPase component−2.225.84
  EAMY_1933oppF, ABC-type oligopeptide transport system−1.636.52
  EAMY_3609dppF, ABC transporter ATP-binding protein−2.435.77
  EAMY_3611dppC, transporter−2.235.73
  EAMY_3610dppD, ABC transporter ATP-binding protein−2.176.15
  EAMY_3613dppA, ABC transporter periplasmic component−2.049.75
  EAMY_3612dppB, ABC transporter−1.946.78
Peptide/Opine/Nickel Uptake Transporter (PepT) Family
  EAMY_1292yliD, ABC-type dipeptide/oligopeptide/nickel transport system−1.556.42
  EAMY_1291yliC, ABC-type dipeptide/oligopeptide/nickel transport system−1.416.66
  EAMY_2311yejA, ABC-type oligopeptide transport system−1.206.22
  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