Protein localization is paramount to protein function, and the intracellular movement of proteins underlies the regulation of numerous cellular processes. Given advances in spatial proteomics, the investigation of protein localization at a global scale has become attainable. Also becoming apparent is the need for dedicated analytical frameworks that allow the discovery of global intracellular protein movement events. Here, we describe TRANSPIRE, a computational pipeline that facilitates TRanslocation ANalysis of SPatIal pRotEomics data sets. TRANSPIRE leverages synthetic translocation profiles generated from organelle marker proteins to train a probabilistic Gaussian process classifier that predicts changes in protein distribution. This output is then integrated with information regarding co-translocating proteins and complexes and enriched gene ontology associations to discern the putative regulation and function of movement. We validate TRANSPIRE performance for predicting nuclear-cytoplasmic shuttling events. Analyzing an existing data set of nuclear and cytoplasmic proteomes during Kaposi Sarcoma-associated herpesvirus (KSHV)-induced cellular mRNA decay, we confirm that TRANSPIRE readily discerns expected translocations of RNA binding proteins. We next investigate protein translocations during infection with human cytomegalovirus (HCMV), a β-herpesvirus known to induce global organelle remodeling. We find that HCMV infection induces broad changes in protein localization, with over 800 proteins predicted to translocate during virus replication. Evident are protein movements related to HCMV modulation of host defense, metabolism, cellular trafficking, and Wnt signaling. For example, the low-density lipoprotein receptor (LDLR) translocates to the lysosome early in infection in conjunction with its degradation, which we validate by targeted mass spectrometry. Using microscopy, we also validate the translocation of the multifunctional kinase DAPK3, a movement that may contribute to HCMV activation of Wnt signaling.

中文翻译：

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TRANSPIRE：从空间蛋白质组数据集中阐明细胞内蛋白质运动的计算管道。

蛋白质定位对于蛋白质功能至关重要，蛋白质的细胞内运动是许多细胞过程调节的基础。鉴于空间蛋白质组学的进步，全球范围内蛋白质定位的研究已成为可能。同样变得明显的是需要专门的分析框架来发现全局细胞内蛋白质运动事件。在这里，我们描述了 TRANSPIRE，一种有助于空间蛋白质组学数据集的易位分析的计算管道。TRANSPIRE 利用细胞器标记蛋白生成的合成易位图谱来训练概率高斯过程分类器，预测蛋白质分布的变化。然后将该输出与有关共易位蛋白质和复合物以及丰富的基因本体关联的信息整合，以辨别运动的假定调节和功能。我们验证了 TRANSPIRE 预测核细胞质穿梭事件的性能。通过分析卡波西肉瘤相关疱疹病毒 (KSHV) 诱导的细胞 mRNA 衰减过程中现有的核和细胞质蛋白质组数据集，我们确认 TRANSPIRE 可以轻松识别 RNA 结合蛋白的预期易位。接下来，我们研究人巨细胞病毒（HCMV）感染期间的蛋白质易位，HCMV 是一种已知可诱导整体细胞器重塑的 β-疱疹病毒。我们发现 HCMV 感染会引起蛋白质定位的广泛变化，预计有 800 多种蛋白质在病毒复制过程中会发生易位。明显的是与 HCMV 对宿主防御、代谢、细胞运输和 Wnt 信号传导的调节相关的蛋白质运动。例如，低密度脂蛋白受体（LDLR）在感染早期易位至溶酶体并同时降解，我们通过靶向质谱法对此进行了验证。使用显微镜，我们还验证了多功能激酶 DAPK3 的易位，这一运动可能有助于 HCMV 激活 Wnt 信号传导。