Exploring The Molecular Mechanism Of Floral Pattern Formation Of Arabidopsis Thaliana By Using Systems Biology Approach

Background: Flower is a suitable experimental system in the process of developmentof plant organ. Research of floral pattern formation is significant to evolution,auxanology and ecology. Arabidopsis thaliana was the first plant that the genomecompletely sequenced. Until now, the functions of30%genes of Arabidopsis thalianaare still unknown. Floral development is a complex process synthetically affected byinternal and external factors. The research which focused on molecular mechanism offloral pattern formation of Arabidopsis thaliana is scarce. To analyze data ofsequences, protein-protein interactions and microarray of different tissues usingsystem biology methods, we hope to explore the molecular mechanism of flowerpattern formation of Arabidopsis thaliana.Methods: In this study, the samples of27non-floral organs and27floral-relatedorgans of Arabidopsis thaliana were chosen from TAIR database. All protein-proteininteraction data, which had been validated by experiments, were downloaded fromBioGRID, IntAct, TAIR, BIND and MINT databases. The sub-cellular localizationinformation derived from SUBA database. Differentially co-expression gene moduleswere found by affy and WGCNA packages of R software and then annotated byClueGO and DAVID. The Hub proteins were analyzed in different modules. Theprotein-protein interaction had been predicted by Support Vector Machine (SVM). Further analysis of the predicted networks, combined with the result of phylogeneticanalysis and the sub-cellular localization, and we rebuilt the related pathways offlower development.Conclusion: Six different modules were found, which include Black, Blue, Brown,Green, Magenta, Red. Using ClueGO and DAVID, we found that there were severaldifferent signal pathways in these modules, which included mRNA metabolize,hormone-mediated signaling pathway, floral organ development and so on in Blackmodule; in Blue module, there were71biology processes, which were divided into5groups, including RNA processing, floral whorl development, carpel development andso on; in Brown module, there were DNA replication initiation, floral organmorphogenesis and so on, which were divided into15groups; in the Green module,there were96processes, which were divided into7groups, including NADPHregeneration, regulation of photosynthesis and so on; in Magenta module, there were10groups which contained109processes, including RNA splicing,photomorphogenesis, negative regulation of flower development and so on; therewere20processes in Red module, and jasmonic acid metabolic process was thesignificant process. We built6weighted protein co-expression networks with the pvalue of module membership and the module’s threshold. Furthermore, we analyzedthe key proteins of each network, and found that some proteins, such as ELF3, COL3,COL4were participated in flowering process of photoperiod pathways. Based on theannotation result, we selected the proteins of flower development and floral organmorphogenesis, respectively, to set up the new protein-protein interaction (PPI)networks, and constructed the phylogenetic tree with the proteins of flowerdevelopment that were derived from literature retrieval. In the process of flowerdevelopment, the flower organ-specific proteins, which included AP1, AP3, AG,SEP3, SEP4et al participated in floral organ morphogenesisvia protein-proteininteraction, and were regulated by ELG, ZFN3, TSO1, RFC3, AT2G27710et alproteins. Integrated the result of phylogenetic analysis, we suggested that ZFN3activated the flower primordial determining gene AP1and AP2by HY5/HYH genevia photoinduction. AT1G77370was a receptor received the signal from extracellular, ELG transduced the signal to the AT2G27710and COI1, which located in cytoplasm.The former activated the nuclear gene TSO1and ELF3, the latter transfer signal byjasmonic acid pathways, regulated the flowering initiation and the expression offlower organ-specific genes.