Small molecule inhibitors suppress expression of both type III secretion and amylovoran biosynthesis genes in Erwinia amylovora

Microarray analysis of E. amylovora treated with compounds no. 3 and no. 9 identified a total of 588 significantly differentially expressed genes. Among them, 95 and 78 genes were, respectively, induced and suppressed by both compounds as compared to DMSO control. Majority of T3SS genes in E. amylovora including hrpL and avrRpt2 effector gene were suppressed by both compounds. Compound no. 3 also suppressed the transcription of amylovoran precursor and biosynthesis genes. On the other hand, both compounds significantly induced expression of glycogen biosynthesis genes and siderophore biosynthesis, regulatory and transport genes. Furthermore, many membrane, lipoprotein and exported protein encoding genes were also activated by both compounds. Erwinia amylovora WT strain treated with compound No. 3 and No. 9 and compared to DMSO control. Four biological replicates for each chemical treatment (two samples were combined) were hybridized to three arrays. Four biological replicates (two each combined) for DMSO treatment were hybridized to two arrays.