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

BMC Genomics

Table 9 List of differentially expressed genes^a associated with DNA repair/replication for the (p) ppGpp⁰ mutant versus WT at 3 h

Accession	Gene Description	Log₂FC	Mean^b
DNA-repair: SOS response
EAMY_2641	recN, DNA repair protein	2.96	9.84
EAMY_3327	lexA, SOS-response transcriptional repressors	2.95	10.27
EAMY_3296	ssb, single-stranded DNA-binding protein	2.22	9.95
EAMY_0882	dinP, DNA polymerase IV	2.15	6.96
EAMY_0805	recA, recombinase A	1.97	11.18
EAMY_2064	ruvA, Holliday junction ATP-dependent DNA helicase	1.66	6.84
EAMY_1211	uvrB, excinuclease UvrABC subunit B	1.56	8.45
EAMY_1251	dinG, ATP-dependent helicase	1.23	7.05
EAMY_2063	ruvB, Holliday junction ATP-dependent DNA helicase	1.18	7.44
EAMY_0194	uvrD, DNA helicase II	1.13	8.55
EAMY_3297	uvrA, excinuclease ATPase subunit	1.01	9.29
DNA replication
EAMY_3296	ssb, single-stranded DNA-binding protein	2.22	9.95
EAMY_2345	gyrA, DNA gyrase A subunit	1.64	10.46
EAMY_0725	exo, 5′-3′ exonuclease	1.47	6.31
EAMY_0844	dnaQ, DNA polymerase III epsilon subunit	1.36	6.88
EAMY_3144	priB, primosomal replication protein N	1.24	10.24
EAMY_1122	holA, DNA polymerase III delta subunit	−1.21	6.86

^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
^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

ISSN: 1471-2164