Advances in Upstream Open Reading Frame in Plant Genes

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

Abstract

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

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.

Figures/Tables 5

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

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）

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

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

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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