Figure 6. Examples of functional linkages in PPI network.

(a) Protein-protein interactions in functional linkage of CO₂ uptake and photosystem II. Sub-network 1 is enriched in photosynthesis, especially photosystem II and carbon dioxide. A key protein, slr1740 (appA, oligopeptide binding protein of ABC transporter) structured a highly important linkage between modules of photosynthesis and carbon dioxide, suggesting the potential function of slr1740 in carbon dioxide uptake and photosystem II. Blue nodes, proteins involved in the photosystem II process; green nodes, proteins involved in CO₂ uptake; pink nodes, first neighbor of CO₂ uptake proteins; yellow node, appA, oligopeptide binding protein of ABC transporter. (b) Protein-protein interactions in biological processes of photosystem II reaction center subunits under UV irradiation. Copies of FtsH (slr1390 and slr1640) separately interacting with their own relative proteins could both link with sml0003 (PS II reaction center M protein), which also interacts with D1 and D2 protein. D1 and D2 proteins then interact with cytochrome proteins, and finally affect slr0008 (CtpA, Carboxyl-terminal processing protease) by a series of PPIs. Blue nodes, FtsH copies; red node photosystem II reaction center M protein; green nodes, protein members of D1 and D2; yellow nodes, cytochrome proteins; pink node, CtpA.