MADS-box transcription factors function as homo- or heterodimers and regulate many aspects of plant development; moreover, MADS-box genes have undergone extensive duplication and divergence. For example, the morphological diversity of floral organs is closely related to the functional divergence of the MADS-box gene family. B-class genes (such as Arabidopsis thaliana APETALA3 [AP3] and PISTILLATA [PI]) belong to a subgroup of MADS-box genes. Here, we collected 97 MADS-box B protein sequences from 21 seed plant species and examined their motifs to better understand the functional evolution of B proteins. We used the MEME tool to identify conserved sequence motifs in these B proteins; unique motif arrangements and sequences were identified in these B proteins. The keratin-like domains of Malus domestica and Populus trichocarpa B proteins differed from those in other angiosperms, suggesting that a novel regulatory network might have evolved in these species. The MADS domains of Nelumbo nucifera, Glycine max, and Amborella trichopoda B-proteins contained motif 9; in contrast, those of other plants contained motif 1. Protein modelling analyses revealed that MADS domains with motif 9 may lack amino acid sites required for DNA-binding. These results suggested that the three species might share an alternative mechanism controlling floral development. Amborella trichopoda has B proteins with either motif 1 or motif 9 MADS domains, suggesting that these two types of MADS domains evolved from the ancestral domain into two groups, those with motif 9 (N. nucifera and G. max), and those with motif 1. Moreover, our results suggest that the homodimer/heterodimer intermediate transition structure first appeared in A. trichopoda. Therefore, our systematic analysis of the motifs in B proteins sheds light on the evolution of these important transcription factors.

中文翻译：

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种子植物 B 类 MADS-box 蛋白基序的进化差异

MADS-box 转录因子作为同源或异源二聚体发挥作用，调节植物发育的许多方面；此外，MADS-box 基因经历了广泛的重复和发散。例如，花器官的形态多样性与MADS-box基因家族的功能差异密切相关。B 类基因（如拟南芥 APETALA3 [AP3] 和 PISTILLATA [PI]）属于 MADS-box 基因的一个亚组。在这里，我们从 21 个种子植物物种中收集了 97 个 MADS-box B 蛋白序列并检查了它们的基序以更好地了解 B 蛋白的功能进化。我们使用 MEME 工具来鉴定这些 B 蛋白中的保守序列基序；在这些 B 蛋白中鉴定出独特的基序排列和序列。Malusdomestica 和 Populus trichocarpa B 蛋白的角蛋白样结构域与其他被子植物中的不同，表明这些物种可能已经进化出一种新的调控网络。Nelumbo nucifera、Glycine max 和 Amborella trichopoda B 蛋白的 MADS 结构域包含基序 9；相比之下，其他植物的那些含有基序 1。蛋白质建模分析表明，具有基序 9 的 MADS 结构域可能缺乏 DNA 结合所需的氨基酸位点。这些结果表明这三个物种可能共享一种控制花发育的替代机制。Amborella trichopoda 的 B 蛋白具有基序 1 或基序 9 MADS 域，这表明这两种类型的 MADS 域从祖先域演化为两组，具有基序 9（N. nucifera 和 G. max）的组和具有基序的组1.此外，我们的结果表明同源二聚体/异源二聚体中间过渡结构首先出现在 A. trichopoda 中。因此，我们对 B 蛋白中基序的系统分析揭示了这些重要转录因子的进化。