Diversifying Evolution of the Ubiquitin-26S Proteasome System in Brassicaceae and Poaceae
Diversifying Evolution of the Ubiquitin-26S Proteasome System in Brassicaceae and Poaceae
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DOI：
10.3390/ijms20133226
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发表时间：
2019-07-01
影响因子：
5.6
通讯作者：
Yu, Peifeng
中科院分区：
文献类型：
--
作者：
Hua, Zhihua;Yu, Peifeng
基因组扩增和序列差异为生物适应提供了原材料。陆地植物中泛素-26 S蛋白酶体系统（UPS）的大量扩增就是例证，其主要依赖于细胞内信号传导和生化代谢来对抗生物和非生物胁迫。虽然一些功能基因组研究已经证明了UPS在植物生长和发育中的适应性作用，但许多UPS成员仍然未知。在这项工作中，我们应用了比较基因组研究，以解决在系统水平上的UPS的功能分歧。我们首先使用了一个关闭目标修剪注释的方法来确定大多数，如果不是全部，UPS成员在六个物种从两个进化上遥远的植物家族，禾本科和禾本科。为了减少与年龄有关的错误，这两组物种是根据它们相似的物种形成时间顺序选择的。通过大小比较、时间扩展推断、进化选择分析、复制机制预测和功能结构域富集测定，我们发现UPS内存在显著差异，特别是来自其三个最大的泛素连接酶基因家族，F-box（FBX）、真正有趣的新基因（RING）和Bric-a-Brac/Tramtrack/Broad Complex（BTB）家族的成员之间，介于禾本科和菊科之间。揭示独立的拟南芥属和水稻属特异性亚基的26 S蛋白酶体亚基从一个全面的系统发育分析进一步支持了一个多样化的进化模型的UPS在这两个属，证实了其在植物适应的作用。
Genome amplification and sequence divergence provides raw materials to allow organismal adaptation. This is exemplified by the large expansion of the ubiquitin-26S proteasome system (UPS) in land plants, which primarily rely on intracellular signaling and biochemical metabolism to combat biotic and abiotic stresses. While a handful of functional genomic studies have demonstrated the adaptive role of the UPS in plant growth and development, many UPS members remain unknown. In this work, we applied a comparative genomic study to address the functional divergence of the UPS at a systematic level. We first used a closing-target-trimming annotation approach to identify most, if not all, UPS members in six species from each of two evolutionarily distant plant families, Brassicaceae and Poaceae. To reduce age-related errors, the two groups of species were selected based on their similar chronological order of speciation. Through size comparison, chronological expansion inference, evolutionary selection analyses, duplication mechanism prediction, and functional domain enrichment assays, we discovered significant diversities within the UPS, particularly between members from its three largest ubiquitin ligase gene families, the F-box (FBX), the Really Interesting New Gene (RING), and the Bric-a-Brac/Tramtrack/Broad Complex (BTB) families, between Brassicaceae and Poaceae. Uncovering independent Arabidopsis and Oryza genus-specific subclades of the 26S proteasome subunits from a comprehensive phylogenetic analysis further supported a diversifying evolutionary model of the UPS in these two genera, confirming its role in plant adaptation.