Evolution of the ARF Gene Family in Land Plants: Old Domains, New Tricks
Evolution of the ARF Gene Family in Land Plants: Old Domains, New Tricks
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DOI：
10.1093/molbev/mss220
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发表时间：
2013-01-01
影响因子：
10.7
通讯作者：
Marletaz, Ferdinand
中科院分区：
文献类型：
--
作者：
Finet, Cedric;Berne-Dedieu, Annick;Marletaz, Ferdinand
生长素反应因子（ARF）是植物生长发育过程中的关键因子。它们通过激活或抑制下游发育基因的表达来介导细胞对植物激素生长素的反应。ARF蛋白的关键激活功能是通过其四结构域结构实现的，其包括DNA结合和蛋白质二聚化基序。为了确定这种特征结构的进化起源，我们建立了一个全面的224个ARF相关蛋白质序列的数据集，这些序列代表了陆地植物的所有主要生活部门，除了金鱼藻。我们发现，ARF分为三个亚科，可以追溯到陆地植物的起源。我们还表明，广泛的基因重复的重复事件有助于扩大这三个原始的亚家族。对我们的数据集的进一步检查发现了ARF转录本结构的广泛多样性，并使我们能够识别ARF蛋白中的额外保守基序。我们发现ARF蛋白的额外结构多样性主要由两种机制产生：基因组截短和选择性剪接。我们建议，从典型的，四域ARF结构的域的损失，促进了ARF家族内的功能转移，破坏二聚化或DNA结合能力。例如，苔藓和穗苔基因组中的一些ARF中的二聚化结构域的丢失导致了使人想起Aux/IAA蛋白的蛋白质，这可能为这些ARF功能调节剂的进化提供了线索。我们还评估了选择性剪接在ARF 4的情况下的功能影响，我们已经确定了一个新的异构体在拟南芥。遗传分析表明，这两个转录本在A. thaliana.因此，基因复制，结构域重排和转录后调控，使生长素信号通过ARF蛋白，可能有助于这些调节剂在植物发育和进化的至关重要的微妙控制。
Auxin response factors (ARF) are key players in plant development. They mediate the cellular response to the plant hormone auxin by activating or repressing the expression of downstream developmental genes. The pivotal activation function of ARF proteins is enabled by their four-domain architecture, which includes both DNA-binding and protein dimerization motifs. To determine the evolutionary origin of this characteristic architecture, we built a comprehensive data set of 224 ARF-related protein sequences that represents all major living divisions of land plants, except hornworts. We found that ARFs are split into three subfamilies that could be traced back to the origin of the land plants. We also show that repeated events of extensive gene duplication contributed to the expansion of those three original subfamilies. Further examination of our data set uncovered a broad diversity in the structure of ARF transcripts and allowed us to identify an additional conserved motif in ARF proteins. We found that additional structural diversity in ARF proteins is mainly generated by two mechanisms: genomic truncation and alternative splicing. We propose that the loss of domains from the canonical, four-domain ARF structure has promoted functional shifts within the ARF family by disrupting either dimerization or DNA-binding capabilities. For instance, the loss of dimerization domains in some ARFs from moss and spikemoss genomes leads to proteins that are reminiscent of Aux/IAA proteins, possibly providing a clue on the evolution of these modulators of ARF function. We also assessed the functional impact of alternative splicing in the case of ARF4, for which we have identified a novel isoform in Arabidopsis thaliana. Genetic analysis showed that these two transcripts exhibit markedly different developmental roles in A. thaliana. Gene duplications, domain rearrangement, and post-transcriptional regulation have thus enabled a subtle control of auxin signaling through ARF proteins that may have contributed to the critical importance of these regulators in plant development and evolution.