Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France.
Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France.
Biochim Biophys Acta Gen Subj. 2019 Oct;1863(10):1458-1470. doi: 10.1016/j.bbagen.2019.05.009. Epub 2019 May 23.
Ghost proteins are issued from alternative Open Reading Frames (ORFs) and are missing a genome annotation. Indeed, historical filters applied for the detection of putative translated ORFs led to a wrong classification of transcripts considered as non-coding although translated proteins can be detected by proteomics. This Ghost (also called Alternative) proteome was neglected, and one major issue is to identify the implication of the Ghost proteins in the biological processes. In this context, we aimed to identify the protein-protein interactions (PPIs) of the Ghost proteins. For that, we re-explored a cross-link MS study performed on nuclei of HeLa cells using cross-linking mass spectrometry (XL-MS) associated with the HaltOrf database. Among 1679 cross-link interactions identified, 292 are involving Ghost Proteins. Forty-Four of these Ghost proteins are found to interact with 7 Reference proteins related to ribonucleoproteins, ribosome subunits and zinc finger proteins network. We, thus, have focused our attention on the heterotrimer between the RE/poly(U)-binding/degradation factor 1 (AUF1), the Ribosomal protein 10 (RPL10) and AltATAD2. Using I-Tasser software we performed docking models from which we could suggest the attachment of AUF1 on the external part of RPL10 and the interaction of AltATAD2 on the RPL10 region interacting with 5S ribosomal RNA as a mechanism of regulation of the ribosome. Taken together, these results reveal the importance of Ghost Proteins within known protein interaction networks.
幽灵蛋白是从替代开放阅读框（ORF）产生的，并且缺少基因组注释。实际上，历史上应用于检测潜在翻译 ORF 的过滤器导致了对被认为是非编码的转录本的错误分类，尽管可以通过蛋白质组学检测到翻译蛋白。这个幽灵（也称为替代）蛋白质组被忽视了，一个主要问题是确定幽灵蛋白在生物过程中的作用。在这种情况下，我们旨在确定幽灵蛋白的蛋白质-蛋白质相互作用（PPIs）。为此，我们重新探索了一项使用交联质谱（XL-MS）结合 HaltOrf 数据库对 HeLa 细胞核进行的交联 MS 研究。在鉴定的 1679 个交联相互作用中，有 292 个涉及幽灵蛋白。其中 44 个幽灵蛋白与 7 个与核糖核蛋白、核糖体亚基和锌指蛋白网络相关的参考蛋白相互作用。因此，我们将注意力集中在异三聚体之间，即 AUF1（RE/poly（U）结合/降解因子 1）、核糖体蛋白 10（RPL10）和 AltATAD2。我们使用 I-Tasser 软件进行对接模型，从中我们可以提出 AUF1 附着在 RPL10 的外部部分，以及 AltATAD2 与 5S 核糖体 RNA 相互作用的 RPL10 区域的相互作用，作为核糖体调节的一种机制。总之，这些结果揭示了幽灵蛋白在已知蛋白质相互作用网络中的重要性。
