Figure 6. Characterization of extra-genic suppressors reverting the biofilm formation defect of ΔrfaY cells in an over-expression library.

(A) Distribution of LPS biosynthesis genes were compared in the ΔrfaY transposon insertion and over-expression libraries. The microarray outputs of the ΔrfaY transposon insertion and the ΔrfaY over-expression libraries were sorted separately based on their z-score and divided into 10 equally populated bins. The number of genes belonging to lipopolysaccharide biosynthesis gene cluster (GO index GO:0009103) in each bin was counted and used to calculate hypergeometric p-value for over-representation of LPS biosynthesis genes in that bin for each library. Each bin was color-coded based on its −log₁₀(p-value). The yellow color for a bin reflects statistically significant abundance of lipopolysaccharide biosynthesis genes in that bin. As shown, many LPS biosynthetic genes were found to be among the top 10% highly enriched category in the ΔrfaY background transposon insertion library, while in the over-expression library they belonged to the top 10% most depleted group. (B) LPS samples extracted from ΔrfaY pBR322-gadXYW and ΔrfaY cells and separated on SDS gels. (C) Transcription level of the rfaQ-K operon promoter is compared between ΔrfaY pBR322-gadWYX and ΔrfaY pBR322 cells by a β-galactosidase assay.