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

Yang, Ho-wen; Yu, Menghao; Lee, Jae Hoon; Chatnaparat, Tiyakhon; Zhao, Youfu

doi:10.1186/s12864-020-6699-5

BMC Genomics

Table 3 List of differentially expressed genes^a associated with motility 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	Log₂FC^b	Mean^c
EAMY_1508	fliI, flagellum-specific ATP synthase	−6.25	6.73
EAMY_1509	fliH, flagellar assembly protein	−5.98	6.74
EAMY_1456	flgE, flagellar hook protein	−5.97	9.06
EAMY_1511	fliF, flagellar M-ring protein	−5.73	7.65
EAMY_1457	flgF, flagellar basal body rod protein	−5.71	7.79
EAMY_1510	fliG, flagellar motor switch protein	−5.66	6.86
EAMY_1453	flgB, flagellar basal body protein	−5.4	7.22
EAMY_1459	flhH, flagellar L-ring protein	−5.33	6.57
EAMY_1455	flgD, flagellar hook capping protein	−5.26	7.96
EAMY_1454	flgC, flagellar basal body rod protein	−5.23	7.01
EAMY_1507	fliJ, flagellar biosynthesis chaperone	−5.22	6.24
EAMY_1505	fliL, flagellar basal body-associated protein	−5.03	6.53
EAMY_1506	fliK, flagellar hook-length control protein	−4.88	7.96
EAMY_1503	fliN, flagellar motor switch protein	−4.77	6.23
EAMY_1458	flgG, flagellar basal body rod protein	−4.71	7.75
EAMY_1504	fliM, flagellar motor switch protein	−4.66	7.17
EAMY_1460	flgI, flagellar P-ring protein	−4.33	6.58
EAMY_1461	flgJ, flagellar rod assembly protein	−4.19	6.49
EAMY_1502	fliO, flagellar biogenesis protein	−4.13	5.93
EAMY_1512	fliE, flagellar hook-basal body protein	−3.67	5.80
EAMY_1501	fliP, flagellar biosynthetic protein	−3.54	6.15
EAMY_1452	flgA, flagellar basal body P-ring biosynthesis protein	−3.3	6.32
EAMY_1500	fliQ, flagellar biosynthetic protein	−2.81	4.63
EAMY_2139	fliA, RNA polymerase sigma factor	−2.41	6.33
EAMY_2138	fliZ, flagellar regulatory protein	−2.15	5.81
EAMY_2143	fliS, flagellin-specific chaperone	−2.08	6.03
EAMY_2144	fliT, flagellar export chaperone	−1.89	5.71
EAMY_2142	fliD, flagellar capping protein	−1.75	7.72
EAMY_2682	fliR, flagellar biosynthetic protein	−1.54	2.85
EAMY_1499	fliR, flagellar biosynthetic protein	−1.5	5.59
EAMY_1463	flgL, flagellar hook-associated protein	−1.28	6.56
EAMY_1462	flgK, flagellar hook-associated protein	−1.25	7.56
EAMY_2660	flgJ, flagellar rod assembly protein	−1.00	2.41
EAMY_2662	flgH3, Flagellar L-ring protein	−1.07	1.70
EAMY_2689	fliK3, flagellar hook-length control protein	−1.06	3.62

^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.
^blog₂FC valus was calculated by the log based 2 value of (p) ppGpp⁰ / WT at 3 h
^cThe average of log₂CPM was calculated. CPM: count per million reads

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ISSN: 1471-2164

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