Wang Sishuo, Chen Youhua
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
Department of Botany, Faculty of Science, The University of British Columbia, Vancouver, BC, Canada.
Front Plant Sci. 2019 May 8;10:534. doi: 10.3389/fpls.2019.00534. eCollection 2019.
Plant genomes are extensively shaped by various types of gene duplication. However, in this active area of investigation, the vast majority of studies focus on the sequence and transcription of duplicate genes, leaving open the question of how translational regulation impacts the expression and evolution of duplicate genes. We explored this issue by analyzing the ribo- and mRNA-seq data sets across six tissue types and stress conditions in and maize (). We dissected the relative contributions of transcriptional and translational regulation to the divergence in the abundance of ribosome footprint (RF) for different types of duplicate genes. We found that the divergence in RF abundance was largely programmed at the transcription level and that translational regulation plays more of a modulatory role. Intriguingly, translational regulation is characterized by its strong directionality, with the divergence in translational efficiency (TE) globally counteracting the divergence in mRNA abundance, indicating partial buffering of the transcriptional divergence between paralogs by translational regulation. Divergence in TE was associated with several sequence features. The faster-evolving copy in a duplicate pair was more likely to show lower RF abundance, which possibly results from relaxed purifying selection compared with its paralog. A considerable proportion of duplicates displayed differential TE across tissue types and stress conditions, most of which were enriched in photosynthesis, energy production, and translation-related processes. Additionally, we constructed a database TDPDG-DB (http://www.plantdupribo.tk), providing an online platform for data exploration. Overall, our study illustrates the roles of translational regulation in fine-tuning duplicate gene expression in plants.
植物基因组受到各种类型基因复制的广泛影响。然而，在这个活跃的研究领域中，绝大多数研究集中在复制基因的序列和转录上，而翻译调控如何影响复制基因的表达和进化这一问题仍未得到解决。我们通过分析拟南芥和玉米六种组织类型及胁迫条件下的核糖体和mRNA测序数据集来探讨这个问题。我们剖析了转录调控和翻译调控对不同类型复制基因核糖体足迹（RF）丰度差异的相对贡献。我们发现，RF丰度的差异在很大程度上是在转录水平上编程的，而翻译调控发挥的更多是调节作用。有趣的是，翻译调控具有很强的方向性，翻译效率（TE）的差异在全球范围内抵消了mRNA丰度的差异，这表明翻译调控对旁系同源基因之间的转录差异起到了部分缓冲作用。TE的差异与几个序列特征有关。复制对中进化较快的拷贝更有可能表现出较低的RF丰度，这可能是与其旁系同源基因相比纯化选择放松所致。相当一部分复制基因在不同组织类型和胁迫条件下表现出不同的TE，其中大部分富集在光合作用、能量产生和翻译相关过程中。此外，我们构建了一个数据库TDPDG-DB（http://www.plantdupribo.tk），提供了一个数据探索的在线平台。总体而言，我们的研究阐明了翻译调控在微调植物复制基因表达中的作用。
