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 1 List of differentially expressed genes^a 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

Accession	Gene Description	Log₂FC^b	Mean^c
T3SS
EAMY_0519	hrpK, pathogenicity locus protein	−2.08	4.91
EAMY_0520	hsvA, Hrp-associated systemic virulence protein	−1.75	3.35
EAMY_0525	hrcU, type III secretion protein	−2.21	4.88
EAMY_0526	hrcT, type III secretion apparatus protein	−2.84	3.67
EAMY_0527	hrcS, type III secretion protein	−3.87	2.55
EAMY_0529	hrcQ, type III secretion system apparatus protein	−2.53	5.50
EAMY_0530	hrpP, type III secretion protein	−4.06	4.70
EAMY_0531	hrpO, type III secretion protein	−5.86	4.53
EAMY_0532	hrcN, type III secretion system ATPase	−5.01	5.61
EAMY_0533	hrpQ, type III secretion system protein	−5.65	5.37
EAMY_0534	hrcV, type III secretion inner-membrane protein	−5.3	6.15
EAMY_0535	hrpJ, type III secretion system protein	−5.00	5.88
EAMY_0536	hrpL, RNA polymerase sigma factor	−5.89	6.20
EAMY_0539	hrpS, sigma-54-dependent enhancer-binding protein	−1.45	6.69
EAMY_0542	hrpA, Hrp pili protein	−6.49	9.12
EAMY_0543	hrpB, type III secretion system protein	−5.86	7.46
EAMY_0544	hrcJ, type III secretion inner-membrane protein	−5.42	6.44
EAMY_0545	hrpD, type III secretion protein	−5.19	4.78
EAMY_0546	hrpE, type III secretion apparatus protein	−3.82	4.29
EAMY_0547	hrpF, type III secretion protein	−5.75	5.74
EAMY_0548	hrpG, type III secretion protein	−5.75	6.26
EAMY_0549	hrcC, type III secretion system outer membrane pore	−4.70	7.37
EAMY_0550	hrpT, type III secretion lipoprotein	−4.11	4.43
EAMY_0551	hrpV, type III secretion protein	−4.07	4.35
EAMY_0552	hrpN, harpin protein	−6.32	7.96
EAMY_0553	orfA, Tir chaperone family protein	−4.38	6.87
EAMY_0554	orfB, avirulence protein	−3.33	5.12
EAMY_0555	orfC, HrpW-specific chaperone	−4.98	6.33
EAMY_0556	hrpW, harpin protein	−6.07	7.36
EAMY_0557	dspE, Hrp secreted pathogenicity-like protein	−4.4	9.23
EAMY_0558	dspF, Hrp secreted pathogenicity-like protein	−2.05	6.23
EAMY_0653	eop2, type III effector	−3.34	6.98
EAMY_3175	avrRpt2, cysteine protease avirulence protein	−1.07	6.20
Amylovora
EAMY_2242	amsL, amylovoran biosynthesis protein	−1.04	5.64
EAMY_2243	amsK, glycosyltransferase	−1.26	5.46
EAMY_2244	amsJ, exopolysaccharide biosynthesis protein	−1.10	5.47
EAMY_2245	amsF, exopolysaccharide biosynthesis protein	−1.48	6.10
EAMY_2247	amsD, Amylovoran biosynthesis glycosyltransferase	−1.03	3.53
EAMY_2248	amsC, exopolysaccharide biosynthesis protein	−1.18	4.53
EAMY_2249	amsB, glycosyltransferase	−1.62	5.59
Levan
EAMY_3695	lscC, levansucrase	−3.60	8.19
EAMY_0559	rlsA, transcriptional regulator	−2.62	4.51

^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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