Integrative Analyses Of Plant Interactomes

Proteins usually perform their functions by interacting with other proteins.Although researches on interactomes have been widely reported,few of them are related to plants.In this thesis,a series of integrative analyses based on plant interactomes were conducted.First,a database of protein interaction sites for Arabidopsis thaliana,AraPPISite,was constucted,which aimed to provide a practical tool for plant scientists.Moreover,plant interactome data were integrated with other types of data to explore two important biological issues,i.e.,the mechanisms of plant-pathogen interactions and the formation of heterosis.The results are elaborated as follows:AraPPISite stored the 3D structures of 3,050 A.thaliana protein-protein interactions(PPIs),of which the 3D structures of 27 PPIs were collected from the Protein Data Bank database,and the 3D structures of 3,023 A.thaliana PPIs were predicted by using two template-based docking methods.For each PPI,AraPPISite not only provided an interactive user interface for browsing the 3D structure and protein interaction sites at atomic resolution,but also listed detailed evolutionary and physicochemical properties of these sites.According to these properties,the key sites could be easily identified.Further,AraPPISite assigned interaction regions at the sequence level,i.e.,domain-domain interactions or domain-motif interactions,to 4,286 PPIs whose 3D structures could not be modeled.AraPPISite is a free and user-friendly database.Users can query or download data,and do not need to register or configure on local machines.AraPPISite is especially suitable for the users with less experience in structural biology or protein bioinformatics.AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html.To analyze the mechanism of plant-pathogen interactions,an integrative analysis was conducted by combining A.thaliana PPI network,A.thaliana-Pseudomonas syringae PPIs,A.thaliana-Hyaloperonospora arabidopsidis PPIs,and A.thaliana gene expression profiles.In this process,a specific dynamic trend of up-regulated differentially expressed genes(DEGs)in relation to the effector targets has been observed.By focusing on characteristic network topology,the author found that the effector targets had higher betweenness centrality and tended to be clustered together in the network.By contrast,the effector targets interacting with the same effectors more densely connected to each other.The results showed that pathogens employed the local impact mode to disrupt the proteins with key positions for global diffusion of information throughout the network.Moreover,up-regulated DEGs at the first time were located closest to the effector targets,and stepped away from the effector targets over time during infection.The results indicated that plants gradually activated the proteins far away from the effector targets to compete with pathogens.In line with this observation,pathogen-susceptible mutants tended to have more DEGs surrounding the effector targets compared with resistant mutants.The author also took initiative to investigate the formation mechanism of heterosis based on the interactome of Oryza sativa.Because only a few O.sativa PPIs have been identified compared with A.thaliana,the interolog and Protein interactions by structural matching(PRISM)methods were used to predict and filter all potential PPIs in F1 hybrid.High-quality O.sativa interactome was obtained,including the PPIs only occurred in F1 hybrid,named F1-specific PPIs.The proteins involved in F1-specific PPIs were defined as F1-specific proteins.The results of functional classification showed that most of F1-specific proteins were enzymes,meaning that F1-specific PPIs were critical component of metabolic pathways.Furthermore,O.sativa metabolic gene clusters were identified.F1-specific proteins tended to be metabolic genes in metabolic gene clusters,which proved again that F1-specific PPIs were widely involved in metabolic pathways.Last but not the least,genome-wide association study was performed,and the genes related to three yield traits in four populations were detected.F1-specific proteins contained a large number of yield-related genes,which implied that F1-specific PPIs made significant contribution to the formation of heterosis.Some existing metabolic pathways could be connected by F1-specific PPIs,and new metabolic pathways may be activated by F1-specific PPIs.Thus,these events may enhance F1 hybrid's adaptation to the environment.In summary,a comprehensive database resource of protein interaction sites for A.thaliana was developed,which would be helpful to enhance the study of plant functional genomics.Moreover,the mechanisms of plant-pathogen interactions and the formation of heterosis were investigated from the perspecitive of interactomes,which were important theoretical interests as well as providing some new hints for disease-resistant and high-yield crop improvement.