植物基因上游开放阅读框的研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2022-0832

摘要/Abstract

摘要：

上游开放阅读框（upstream open reading frame, uORF）是一类能够精确控制蛋白质翻译的mRNA元件，位于mRNA的5'端前导区，主要通过抑制翻译起始来调节下游主体开放阅读框（main open reading frame, mORF）的翻译。目前对植物uORF的预测和鉴定主要集中于生物信息学和翻译组学鉴定技术。植物uORF广泛参与调节生长发育、营养代谢、抗病免疫等多个生命活动过程。本文对植物uORF的分类、功能机制、预测和鉴定方法、植物规避uORF的方式以及植物uORF的工程应用等进行综述归纳，旨在更系统和深入地理解植物uORF的功能与机制，并为uORF应用于作物分子育种工作提供参考。

关键词: uORF, 翻译调控, 核糖体, 生长发育, 作物育种

Abstract:

uORF（upstream open reading frame）is a kind of mRNA element that can accurately control protein translation. It is located in the 5' leader region of mRNA. It has been reported to regulate the translation rate of downstream mORF（main open reading frame）by inhibiting the initiation of translation. Currently, the prediction and identification of plant uORF mainly focus on bioinformatics prediction and translatomics identification technology. uORF has regulatory roles on plants in many aspects, such as growth and development, nutrition and metabolism, disease resistance and immunity. In this review, we summarize the classification, functional mechanism, prediction and identification methods of plant uORF, strategies for plants to evade uORF, and the application progress of plant uORF in engineering. The purpose of this paper is to gain a more systematic and in-depth understanding of the function and mechanism of plant uORFs, and to provide a reference for the application of uORF in crop molecular breeding.

Key words: uORF, translational regulation, ribosome, growth and development, crop breeding

薛皦, 朱庆锋, 冯彦钊, 陈沛, 刘文华, 张爱霞, 刘勤坚, 张琪, 于洋. 植物基因上游开放阅读框的研究进展[J]. 生物技术通报, 2023, 39(4): 157-165.

XUE Jiao ZHU Qing-feng FENG Yan-zhao CHEN Pei LIU Wen-hua ZHANG Ai-xia LIU Qin-jian ZHANG Qi YU Yang. Advances in Upstream Open Reading Frame in Plant Genes[J]. Biotechnology Bulletin, 2023, 39(4): 157-165.

图/表 5

图1 植物uORF分类 A：uORF独立于mORF; B：uORF终止于mORF读码框内; C：uORF和mORF终止位置相同; D：混合型uORF

Fig. 1 Upstream open reading frame（uORF）classifica-tions in plant A: The location of the stop codon of the uORF is independent of the mORF. B: The stop codon of the uORF overlaps with the mORF. C: The stop codon of the uORF is the same as that of the stop codon of the mORF. D: Multiple uORFs

图2 植物uORF对mORF的调控方式 A：核糖体渗漏扫描; B：核糖体在mORF处重起始翻译; C：核糖体解离; D：NMD

Fig. 2 Regulatory mechanisms of uORF to mORF A: Leaky scanning by 40S ribosome subnit. B: Translational reinitiation at mORF. C: Ribosome dissociates from the mRNA; D: Trigger nonsense-mediated mRNA decay（NMD）

表1 预测uORF的实验方法比较

Table 1 Comparison of the methods for predicting uORFs

方法比较 Comparison of methods	多聚核糖体分析技术 Polysome profiling	核糖体-新生肽链复合物测序 RNC-Seq	核糖体图谱分析技术 Ribo-seq	核糖体亲和纯化技术 RAP
分离原理	蔗糖密度梯度离心	单一浓度蔗糖溶液离心	RNA酶降解未被核糖体覆盖的mRNA后经蔗糖梯度离心	亲和标签免疫沉淀
分离对象	多聚核糖体复合物	核糖体-新生肽链复合物	被核糖体覆盖保护的RNA小片段	核糖体大亚基及其结合的mRNA
优点	可对核糖体数分组进行收集分析	RNA回收容易，得率高	准确度高，通量大	可组织特异性检测
检测方法	高通量测序或芯片技术	高通量测序或芯片技术	高通量测序	高通量测序或芯片技术
检测的mRNA长度	全长	全长	被核糖体覆盖的约30 nt	全长
缺点	仪器贵重、操作繁琐、RNA回收难度大、纯度低	仪器贵重、无法分析结合不同数量核糖体的 mRNA	操作复杂、酶切条件难控制	需构建转基因植株

图3 植物规避uORF调节的方式 A：选择可变转录起始位点; B：可变剪切排除或修剪uORF; C：不依赖于5'帽子结构的翻译起始

Fig. 3 Mechanisms for evading uORF-mediated regulation A: Alternative transcription start site（TSS）selection. B: Processing uORF by alternative splicing. C: Cap-independent translational initiation

图4 应用uORF操控基因翻译 A：删除uORF上游及翻译起始序列; B：编辑突变uORF的翻译起始位点; C：基因工程手段利用uORF序列

Fig. 4 Manipulation of gene translation by editing uORFs A: Involved the deletion of uORF upstream sequence and initiation codon. B: Involved the mutation of uORF initiation codon. C: Utilized uORF sequence by genetic engineering

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