Xie Wenchuan, Huang Junfeng, Liu Yang, Rao Jianan, Luo Da, He Miao
School of Life Sciences, Sun Yat-Sen University Guangzhou, China.
Front Plant Sci. 2015 Oct 13;6:829. doi: 10.3389/fpls.2015.00829. eCollection 2015.
Flowering is one of the important defining features of angiosperms. The initiation of flower development and the formation of different floral organs are the results of the interplays among numerous genes. But until now, just fewer genes have been found linked with flower development. And the functions of lots of genes of Arabidopsis thaliana are still unknown. Although, the quartet model successfully simplified the ABCDE model to elaborate the molecular mechanism by introducing protein-protein interactions (PPIs). We still don't know much about several important aspects of flower development. So we need to discriminate even more genes involving in the flower development. In this study, we identified seven differentially modules through integrating the weighted gene co-expression network analysis (WGCNA) and Support Vector Machine (SVM) method to analyze co-expression network and PPIs using the public floral and non-floral expression profiles data of Arabidopsis thaliana. Gene set enrichment analysis was used for the functional annotation of the related genes, and some of the hub genes were identified in each module. The potential floral organ morphogenesis genes of two significant modules were integrated with PPI information in order to detail the inherent regulation mechanisms. Finally, the functions of the floral patterning genes were elucidated by combining the PPI and evolutionary information. It was indicated that the sub-networks or complexes, rather than the genes, were the regulation unit of flower development. We found that the most possible potential new genes underlining the floral pattern formation in A. thaliana were FY, CBL2, ZFN3, and AT1G77370; among them, FY, CBL2 acted as an upstream regulator of AP2; ZFN3 activated the flower primordial determining gene AP1 and AP2 by HY5/HYH gene via photo induction possibly. And AT1G77370 exhibited similar function in floral morphogenesis, same as ELF3. It possibly formed a complex between RFC3 and RPS15 in cytoplasm, which regulated TSO1 and CPSF160 in the nucleus, to control the floral organ morphogenesis. This process might also be fine tuning by AT5G53360 in the nucleus.
开花是被子植物重要的界定特征之一。花发育的起始以及不同花器官的形成是众多基因相互作用的结果。但到目前为止，仅有较少的基因被发现与花发育相关。而且拟南芥许多基因的功能仍然未知。尽管四重奏模型通过引入蛋白质 - 蛋白质相互作用（PPI）成功简化了ABCDE模型以阐述分子机制。但我们对花发育的几个重要方面仍然了解不多。所以我们需要鉴别出更多参与花发育的基因。在本研究中，我们通过整合加权基因共表达网络分析（WGCNA）和支持向量机（SVM）方法，利用拟南芥公开的花和非花表达谱数据来分析共表达网络和PPI，鉴定出了七个差异模块。基因集富集分析用于相关基因的功能注释，并在每个模块中鉴定出了一些枢纽基因。将两个重要模块的潜在花器官形态发生基因与PPI信息整合，以详细阐述内在调控机制。最后，通过结合PPI和进化信息阐明了花模式形成基因的功能。结果表明，子网络或复合体而非基因是花发育的调控单元。我们发现拟南芥中最有可能潜在的参与花模式形成的新基因是FY、CBL2、ZFN3和AT1G77370；其中，FY、CBL2作为AP2的上游调节因子；ZFN3可能通过光诱导经由HY5/HYH基因激活花原基决定基因AP1和AP2。并且AT1G77370在花形态发生中表现出与ELF3类似的功能。它可能在细胞质中与RFC3和RPS15形成复合体，在细胞核中调控TSO1和CPSF160，以控制花器官形态发生。这个过程可能也受到细胞核中AT5G53360的精细调节。
