Alternative splicing and translation play important roles in hypoxic germination in rice

First author: Mo-Xian Chen; Affiliations: Shandong Agricultural University (山东农业大学): Taian, China

Corresponding author: Ying-Gao Liu

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination (低氧萌发) of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.

转录后机制PTM包括可变剪切和可变翻译起始可能揭示了参与植物发育和胁迫响应的蛋白的多样性。转录调控对于水稻种子低氧萌发是十分重要的，但PTM在这个过程中的作用还不清楚。本文中，作者通过蛋白组学和RNA测序发现了可变剪切与可变翻译起始如何作用于植物响应低氧胁迫的。作者共鉴定了10253个含有内含子的基因。这些基因中，1741个基因具有差异性表达的可变剪切事件，其中811个基因相比于对照在低氧处理的种子中可变剪切具有差异表达。超过95%的这些基因并不包含在差异表达的基因中。另外，剪接体、核糖体、内质网蛋白加工与输出、蛋白酶体、吞噬体、氧化磷酸化和mRNA监视等调控通路在低氧胁迫中存在可变剪切的变化，说明可变剪切的响应很大程度上是独立于转录调控的。作者鉴定到了相当多的可变剪切变化，包括一些非传统剪切位点的优先使用和差异性表达可变剪切数据集中剪切因子的富集。综上，本文的结果不仅揭示了可变剪切和可变翻译起始在低氧条件下种子萌发过程中发挥重要作用，同时也鉴定了很多通过可变翻译起始产生的新的蛋白或多肽。

通讯：刘鹰高  (http://life.sdau.edu.cn/2018/0316/c2453a123565/page.htm)

个人简介：2005年，兰州大学，硕士；2009年，香港浸会大学，博士。

研究方向：玉米优异逆境相关基因的克隆和功能研究；植物选择性剪切机理及功能研究

doi: https://doi.org/10.1093/jxb/ery393

Journal: Journal of Experimental Botany

First Published: 10 December, 2018