Hubs and bottlenecks in plant molecular signalling networks

Summary Conditional control of plant cell function and development relies on appropriate signal perception, signal integration and processing. The development of high throughput technologies such as proteomics and interactomics has enabled the identification of protein interaction networks that mediate signal processing from inputs to appropriate outputs. Such networks can be depicted in graphical representations using nodes and edges allowing for the immediate visualization and analysis of the network’s topology. Hubs are network elements characterized by many edges (often degree grade k ≥ 5) which confer a degree of topological importance to them. The review introduces the concept of networks, hubs and bottlenecks and describes four examples from plant science in more detail, namely hubs in the redox regulatory network of the chloroplast with ferredoxin, thioredoxin and peroxiredoxin, in mitogen activated protein (MAP) kinase signal processing, in photomorphogenesis with the COP9 signalosome, COP1 and CDD, and monomeric GTPase function. Some guidance is provided to appropriate internet resources, web repositories, databases and their use. Plant networks can be generated from existing public databases and this type of analysis is valuable in support of existing hypotheses, or to allow for the generation of new concepts or ideas. However, intensive manual curating of in silico networks is still always necessary. Contents Summary 919 I. Introduction 920 II. The emergence of the concept of the hub and bottleneck 921 III. General properties of protein–protein interaction hubs and bottlenecks 922 IV. Date vs party hubs in networks 923 V. Structural basis for multiple interactions of hub proteins 923 VI. Bottlenecks in networks 923 VII. Global network analysis of protein–protein interactions in plants 924 VIII. Protein hubs in the cellular redox signalling network 928 IX. Mitogen‐activated protein (MAP) kinases as signalling hubs 929 X. Hubs in photomorphogenesis 930 XI. Monomeric GTPases 932 XII. Towards quantitative characterization of signalling hubs 933 XIII. Outlook 933 Acknowledgements 934 References 934