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Table 1 List of differentially expressed genesa associated with virulence 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
T3SS
EAMY_0519hrpK, pathogenicity locus protein−2.084.91
EAMY_0520hsvA, Hrp-associated systemic virulence protein−1.753.35
EAMY_0525hrcU, type III secretion protein−2.214.88
EAMY_0526hrcT, type III secretion apparatus protein−2.843.67
EAMY_0527hrcS, type III secretion protein−3.872.55
EAMY_0529hrcQ, type III secretion system apparatus protein−2.535.50
EAMY_0530hrpP, type III secretion protein−4.064.70
EAMY_0531hrpO, type III secretion protein−5.864.53
EAMY_0532hrcN, type III secretion system ATPase−5.015.61
EAMY_0533hrpQ, type III secretion system protein−5.655.37
EAMY_0534hrcV, type III secretion inner-membrane protein−5.36.15
EAMY_0535hrpJ, type III secretion system protein−5.005.88
EAMY_0536hrpL, RNA polymerase sigma factor−5.896.20
EAMY_0539hrpS, sigma-54-dependent enhancer-binding protein−1.456.69
EAMY_0542hrpA, Hrp pili protein−6.499.12
EAMY_0543hrpB, type III secretion system protein−5.867.46
EAMY_0544hrcJ, type III secretion inner-membrane protein−5.426.44
EAMY_0545hrpD, type III secretion protein−5.194.78
EAMY_0546hrpE, type III secretion apparatus protein−3.824.29
EAMY_0547hrpF, type III secretion protein−5.755.74
EAMY_0548hrpG, type III secretion protein−5.756.26
EAMY_0549hrcC, type III secretion system outer membrane pore−4.707.37
EAMY_0550hrpT, type III secretion lipoprotein−4.114.43
EAMY_0551hrpV, type III secretion protein−4.074.35
EAMY_0552hrpN, harpin protein−6.327.96
EAMY_0553orfA, Tir chaperone family protein−4.386.87
EAMY_0554orfB, avirulence protein−3.335.12
EAMY_0555orfC, HrpW-specific chaperone−4.986.33
EAMY_0556hrpW, harpin protein−6.077.36
EAMY_0557dspE, Hrp secreted pathogenicity-like protein−4.49.23
EAMY_0558dspF, Hrp secreted pathogenicity-like protein−2.056.23
EAMY_0653eop2, type III effector−3.346.98
EAMY_3175avrRpt2, cysteine protease avirulence protein−1.076.20
Amylovora
EAMY_2242amsL, amylovoran biosynthesis protein−1.045.64
EAMY_2243amsK, glycosyltransferase−1.265.46
EAMY_2244amsJ, exopolysaccharide biosynthesis protein−1.105.47
EAMY_2245amsF, exopolysaccharide biosynthesis protein−1.486.10
EAMY_2247amsD, Amylovoran biosynthesis glycosyltransferase−1.033.53
EAMY_2248amsC, exopolysaccharide biosynthesis protein−1.184.53
EAMY_2249amsB, glycosyltransferase−1.625.59
Levan
EAMY_3695lscC, levansucrase−3.608.19
EAMY_0559rlsA, transcriptional regulator−2.624.51
  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.
  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