Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline
Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline
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DOI：
10.1016/j.molp.2020.05.012
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发表时间：
2020-07-06
期刊：
影响因子：
27.5
通讯作者：
Wu, Liuji
中科院分区：
文献类型：
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作者：
Wang, Shunxi;Tian, Lei;Wu, Liuji
非常规肽（Non-conventional peptides，NCP）是一类由开放阅读码框编码的小肽，在生物学过程中起着重要作用。本研究利用高通量质谱技术构建了一个完整的肽基因组管道，并将其应用于植物NCPs的大规模鉴定，在玉米和拟南芥中分别鉴定了1993个和1860个NCPs。与传统肽相比，这些NCP显示出独特的特征，并且来自内含子、3'UTR、5' UTR、连接和基因间区域。此外，我们的研究结果表明，翻译事件在未注释的成绩单发生更广泛的比以前认为的。此外，我们发现，几十个玉米NCP富集在与表型变异和驯化选择相关的区域内，这表明它们可能参与玉米复杂性状的遗传调控和驯化。总之，我们的研究开发了一个集成的肽基因组管道，用于大规模鉴定植物中的NCP，这将有助于从其他植物中全面表征NCP。在单子叶植物（玉米）和双子叶植物（拟南芥）中发现了大规模的NCPs，表明植物基因组中的大部分基因可以被翻译成具有生物学功能的分子，这对功能基因组研究具有重要意义。
Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns, 3' UTRs, 5' UTRs, junctions, and intergenic regions. Furthermore, our results showed that translation events in unannotated transcripts occur more broadly than previously thought. In addition, we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection, indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize. Taken together, our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants, which would facilitate global characterization of NCPs from other plants. The identification of large-scale NCPs in both monocot (maize) and dicot (Arabidopsis) plants indicates that a large portion of plant genome can be translated into biologically functional molecules, which has important implications for functional genomic studies.