Fig. 4
From: Network biology discovers pathogen contact points in host protein-protein interactomes
Experimental validation of the key proteins in CSILRR. a CSILRR network is organized using Edge-weighted spring embedded layout (left) and weighted k-shell decomposition analysis (right). Internal layers of CSILRR proteins are annotated to the right (red). Venn diagram shows the overlap of 23 out of 35 nodes belonging to internal layers of CSILRR with MTI subnetwork. b, c Distribution of average degree (r2 = 0.9, Mann–Whitney–Wilcoxon test P = 2.43 × 10−15) (b) and average information centrality (IC; c) (r2 = 0.93, Mann–Whitney–Wilcoxon test P < 2.2 × 10−16) for each shell laid out from the core to the periphery of CSILRR network. d Pairwise yeast two-hybrid (Y2H) experiment between kinase domains of 20 LRR-RKs and 31 effectors from Pseudomonas syringae pv. tomato DC3000. An equal amount of mated diploid yeast is spotted on minimum synthetic medium dropouts SD-LT (leucine and tryptophan), SD-LTH (leucine, tryptophan, and histidine), and SD-LH (leucine and histidine + cycloheximide). SD-LTH ansd SD-LH media were supplemented with 1 mM 3-Amino-1,2,4-Triazol (3AT). Positive and negative interactions are determined based on growth and no growth on SD-LTH and SD-LH media, respectively. The identity of an LRR-RK and a particular effector for an interacting pair is revealed. e Phenotypic enrichment analyses among the nodes of effector targets (red) and non-targets (blue) among LRR-RKs belong to internal and peripheral layers CSILRR proteins are shown (hypergeometric P < 0.05). f Split-YFP interaction assay in protoplasts derived from wild-type leaves. The percentage of positive cells was calculated by dividing the number of fluorescing cells by the total number of cells within an image (indicated values = mean ± S.E.M.; six biological replications). N designates the number of cells evaluated. Representative photos of the positive interactions are shown. The CD3−1089::ADF4 (Arabidopsis Actin Depolymerizing Factor 4) and CD3−1096::MBP (maltose binding protein of E. coli) interaction was used as a positive control. Empty CD3−1089 and CD3−1096 vectors were used as a negative control in each independent transformation
