Getting to the edge: protein dynamical networks as a new frontier in plant-microbe interactions

Abstract

A systems perspective on diverse phenotypes, mechanisms of infection, and responses to environmental stresses can lead to considerable advances in agriculture and medicine. A significant promise of systems biology within plants is the development of disease-resistant crop varieties, which would maximize yield output for food, clothing, building materials, and biofuel production. A systems or "-omics" perspective frames the next frontier in the search for enhanced knowledge of plant network biology. The functional understanding of network structure and dynamics is vital to expanding our knowledge of how the intercellular communication processes are executed. This review article will systematically discuss various levels of organization of systems biology beginning with the building blocks termed "-omes" and ending with complex transcriptional and protein-protein interaction networks. We will also highlight the prevailing computational modeling approaches of biological regulatory network dynamics. The latest developments in the "-omics" approach will be reviewed and discussed to underline and highlight novel technologies and research directions in plant network biology.

Keywords: edgetics; functional modules; network dynamics; plant–pathogen interactions; protein–protein interactions; regulatory network; systems biology.

FIGURE 1

The systems biology approaches to understand plant immune systems. (A) The diagrammatic overview of the integrative framework of multiple layers of “-omics” including genomics, transcriptomics, proteomics and phonemics. (B) Visualization of a cell as a complex web of macromolecular interactions that constitutes an “interactome.” Functional modules, such as transcriptional (protein–DNA interactions; PDI), translational (protein–protein interactions; PPI) and metabolic (metabolite–compound interactions; MCI) are illustrated.

FIGURE 2

Network structure and topology. (A) The organization of nodes and edges in a graph represents network structure. Vertices and links represent nodes and edges, respectively. Two nodes can be connected by undirected or directed edges. (B) A sub-network of plant–pathogen interactions is demonstrated. Hubs (highly connected proteins), bottlenecks (high betweenness nodes), and pathogen effectors (virulence factors) are depicted in red, yellow, and brown colors, respectively. Network with scale-free topology might be vulnerable to pathogen-mediated perturbations.