Zhang Shu-Dong, Ling Li-Zhen, Zhang Quan-Fang, Xu Jian-Di, Cheng Le
Germplasm Bank of Wild Species, Kunming, 650201, China.
BGI-Yunnan, BGI-Shenzhen, Kunming, 650106, China.
PLoS One. 2015 Apr 24;10(4):e0124621. doi: 10.1371/journal.pone.0124621. eCollection 2015.
A complete picture of the evolution of miRNA combinatorial regulation requires the synthesis of information on all miRNAs and their targets. MiR156 and miR529 are two combinatorial regulators of squamosa promoter binding protein-like (SBP-box) genes. Previous studies have clarified the evolutionary dynamics of their targets; however, there have been no reports on the evolutionary patterns of two miRNA regulators themselves to date. In this study, we investigated the evolutionary differences between these two miRNA families in extant land plants. Our work found that miR529 precursor, especially of its mature miRNA sequence, has a higher evolutionary rate. Such accelerating evolution of miR529 has significantly effects on its structural stability, and sequence conservation against existence of itself. By contrast, miR156 evolves more rapidly in loop region of the stable secondary structure, which may contribute to its functional diversity. Moreover, miR156 and miR529 genes have distinct rates of loss after identical duplication events. MiR529 genes have a higher average loss rate and asymmetric loss rate in duplicated gene pairs, indicating preferred miR529 gene losses become another predominant mode of inactivation, that are implicated in the contraction of this family. On the contrary, duplicated miR156 genes have a low loss rate, and could serve as another new source for functional diversity. Taken together, these results provide better insight into understanding the evolutionary divergence of miR156 and miR529 family in miRNA combinational regulation network.
要全面了解miRNA组合调控的进化过程，需要综合所有miRNA及其靶标的信息。MiR156和MiR529是鳞状启动子结合蛋白样（SBP-box）基因的两个组合调控因子。先前的研究已经阐明了它们靶标的进化动态；然而，迄今为止，尚未有关于这两个miRNA调控因子自身进化模式的报道。在本研究中，我们调查了现存陆地植物中这两个miRNA家族之间的进化差异。我们的研究发现，MiR529前体，尤其是其成熟的miRNA序列，具有更高的进化速率。MiR529的这种加速进化对其结构稳定性以及自身存在时的序列保守性有显著影响。相比之下，MiR156在稳定二级结构的环区进化更快，这可能有助于其功能多样性。此外，MiR156和MiR529基因在相同的复制事件后具有不同的丢失率。MiR529基因在复制基因对中的平均丢失率和不对称丢失率更高，表明MiR529基因的优先丢失成为另一种主要的失活模式，这与该家族的收缩有关。相反，复制的MiR156基因丢失率较低，并且可以作为功能多样性的另一个新来源。综上所述，这些结果为理解miR156和MiR529家族在miRNA组合调控网络中的进化差异提供了更好的见解。
