Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae
Fig 6
Topological parameters and predictive power of the signal-specific KEI networks.
A. Comparison of the distribution of the shortest path length in the signal-specific networks D29E, D29E + HopA1, D29E + HopAF1, D29E + HopAI1, and D29E + AvrPto shown in 5C. Frequency of path length (of one to six nodes) was calculated using the NetworkAnalyzer [78] in Cytoscape 3.6.1. B–C. Sub-graphs of essential nodes in the defense signal-specific networks (B: cumulated HopA1, HopAI1, HopAF1, and AvrPto) and cell death networks (C: cumulated HopQ1-1, MKK7, and MKK9) (E) networks (shown in Fig 5C), computed using the topological scoring method of MCC. The MCC score is visualized in the node size and color (larger, darker color → higher score). MCC was computed using the cytoHubba app [79] and visualized using Cytoscape 3.6.1. D. Scoring of cell death in Nicotiana benthamiana leaves silenced for individual kinases and challenged with the nonhost pathogen Pseudomonas fluorescens, followed by the avirulent pathogen DC3000. Percentages of infiltrated areas showing various intensities of cell death are plotted for plants silenced for KEIs or with a control plasmid (EC1). Cell death was scored as absent (0%–25% death in the infiltrated area), partial (26%–75% cell death), or full (76%–100%). N shows the total number of replicates for each line tested. E. Bubble plot visualizing the cell death intensity and regulatory strength (−log10 of p-value) of KEIs tested in D. Blue bubbles show KEIs with statistically significant p-values; off-white bubble KEIs showed no statistical difference compared with the EC1 control. The size of bubbles is proportional with N shown in D. F. A weighted interaction network of Arabidopsis homologs of KEIs based on curated associations downloaded from STRING v10 [80]. Edges represent PPIs (continuous lines) or co-expression (interrupted lines). Edge weights are proportional with confidence scores calculated in STRING v10, scaled between zero and one, and indicating the likelihood that interactions are biologically meaningful, specific, and reproducible. Edge labels indicate the signal-specific networks in which connected KEIs are co-occurring. CD, cell death; KEI, Kinase Effector Interactor; MCC, Maximal Clique Centrality; PPI, protein–protein interaction.