Herrera-Ubaldo Humberto, Campos Sergio E, López-Gómez Pablo, Luna-García Valentín, Zúñiga-Mayo Víctor M, Armas-Caballero Gerardo E, González-Aguilera Karla L, DeLuna Alexander, Marsch-Martínez Nayelli, Espinosa-Soto Carlos, de Folter Stefan
Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México.
Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato 36824, México.
Mol Plant. 2023 Jan 2;16(1):260-278. doi: 10.1016/j.molp.2022.09.004. Epub 2022 Sep 9.
Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors (TFs). The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development. The gynoecium is the flower's female reproductive part, crucial for fruit and seed production and, hence, for reproductive success. After the establishment of carpel identity, many tissues arise to form a mature gynoecium. TFs have been described as regulators of gynoecium development, and some interactions and complexes have been identified. However, broad knowledge about the interactions among these TFs and their participation during development remains scarce. In this study, we used a systems biology approach to understand the formation of a complex reproductive unit-as the gynoecium-by mapping binary interactions between well-characterized TFs. We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions (PPIs), resulting in a process-specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. In addition, we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs. Furthermore, we analyzed the network by combining PPI data, expression, and genetic data, which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes. Finally, we generated an extended PPI network that predicts new players in gynoecium development. Taken together, all these results serve as a valuable resource for the plant community.
花由一些器官组成，这些器官的特性由转录因子（TFs）的组合活性所定义。MADS盒转录因子之间的相互作用以及蛋白质复合物的形成已在花发育的花四重奏模型中得以示意。雌蕊群是花的雌性生殖部分，对果实和种子的产生至关重要，因此对繁殖成功也至关重要。在确定心皮特性后，许多组织发育形成成熟的雌蕊群。转录因子已被描述为雌蕊群发育的调节因子，并且已经确定了一些相互作用和复合物。然而，关于这些转录因子之间的相互作用及其在发育过程中的参与情况的广泛知识仍然匮乏。在本研究中，我们采用系统生物学方法，通过绘制已充分表征的转录因子之间的二元相互作用来了解复杂生殖单位——雌蕊群的形成。我们分析了近4500种组合，检测到250多种蛋白质-蛋白质相互作用（PPI），从而生成了一个特定过程的相互作用图谱。拓扑分析揭示了许多转录因子的潜在功能和新作用。此外，我们观察到参与生长素和细胞分裂素信号通路的转录因子与其他转录因子之间存在密切关系。此外，我们通过结合PPI数据、表达数据和遗传数据来分析该网络，这有助于我们将其分解为与雌蕊群发育过程相关的几个动态时空子网。最后，我们生成了一个扩展的PPI网络，该网络预测了雌蕊群发育中的新参与者。综上所述，所有这些结果为植物学界提供了宝贵的资源。
