Distinct types of short open reading frames are translated in plant cells
Distinct types of short open reading frames are translated in plant cells
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DOI：
10.1101/213736
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发表时间：
2017-11
期刊：
影响因子：
7
通讯作者：
I. Fesenko;I. Kirov;A. Kniazev;R. Khazigaleeva;V. Lazarev;Daria Kharlampieva;E. Grafskaia;V. Zgoda-V.-Z
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作者：
I. Fesenko;I. Kirov;A. Kniazev;R. Khazigaleeva;V. Lazarev;Daria Kharlampieva;E. Grafskaia;V. Zgoda-V.-Z
基因组包含数百万个短（<100个密码子）开放阅读框（sORF），这些sORF通常在基因注释过程中被忽略。尽管如此，由这样的sORF编码的肽可以发挥重要的生物学作用，它们对细胞过程的影响长期被低估。在这里，我们分析了模式植物小立碗藓（苔藓）中大约70，000个转录的sORF。苔藓基因组中存在几类不同的sORF，它们在转录本上的位置和进化保守水平不同。超过5000个sORFs被保存在至少一个10种植物物种检查。蛋白质组和肽组数据集的质谱分析表明，位于mRNA和长非编码RNA（lncRNA）的不同部分的602个sORF被翻译，其中包括74个保守的sORF。对sORF和来自单个基因的主ORF的翻译的组合分析表明存在具有组织特异性表达的双顺反子和多顺反子mRNA。选择性剪接可能涉及从此类转录物中切除可翻译的sORF。我们鉴定了一组与已知蛋白质结构域同源的sORF，并认为它们具有小干扰肽的功能。候选lncRNA编码肽的功能分析表明，它参与调节苔藓的生长和分化。sORFs的高进化速率和广泛的翻译表明它们可能提供潜在活性肽的储存库以及它们作为基因进化原料的重要性。因此，我们的研究结果为在植物界发现新的生物活性肽开辟了新的途径。
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in atleast one of ten plant species examined. Mass spectrometry analysis of proteomic and peptidomic datasets suggested that 602 sORFs located on distinct parts of mRNAs and long non-coding RNAs (lncRNAs) are translated, including 74 conservative sORFs. Combined analysis of the translation of the sORFs and the main ORF from a single gene suggested the existence of bi- and poly-cistronic mRNAs with tissue-specific expression. Alternative splicing is likely involved in the excision of translatable sORFs from such transcripts. We identified a group of sORFs homologous to known protein domains and suggested they function as small interfering peptides. Functional analysis of a candidate lncRNA-encoded peptide showed it to be involved in regulating growth and differentiation in moss. The high evolutionary rate and wide translation of sORFs suggest that they may provide a reservoir of potentially active peptides and their importance as a raw material for gene evolution. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.