Data in the identification of poly I:C interacted proteins and their regulation in transcription level against bacterial infection in zebrafish.

To identify target proteins that bind with poly I:C in fish, zebrafish were homogenated to isolate. Resin-immobilized poly I:C was used to capture target proteins in the bacterial protein extracts. These binding proteins were separated by SDS-PAGE and identified by LC-MS/MS. Totally,27 proteins were determined. These results indicate that at least 27 proteins are bound with poly I:C.Then GO terms enrichment was used to analyze these poly I:C-bound proteins. In cellular component enrichment, these proteins are classified to cytoplasm, plasma membrane, cytoskeleton, extracellular region, troponin complex, hemoglobin complex, cytosolic large ribosomal subunit, and ATP synthase complex. In molecular function enrichment, these proteins work for oxygen binding, ATP binding, calcium ion binding, actin filament binding, phospholipid binding, ubiquitin-protein transferase activity, kinase activity, oxidoreductase activity, histone binding, signaling receptor complex adaptor activity, lysozyme activity, protein-disulfide reductase activity, and structural constituent of ribosome. In biological process enrichment, these proteins belong to ubiquitin-dependent protein catabolic process, oxygen transport, muscle contraction, reverse cholesterol transport, hydrolase activity, actin filament organization, cytoplasmic translational elongation, regulation of mitochondrial fusion, regulation of apoptotic process, cytosolic ribosome assembly, proton motive force-driven ATP synthesis, peptidyl-proline hydroxylation to 4-hydroxy-L-proline, G protein-coupled receptor signaling pathway, and structural molecule activity. Therefore, these poly I:C-bound proteins cover many aspects of cell activities. We further analyzed the predicted PPI network of these poly I:C-bound proteins using STRING software and then clustered them using the MCL algorithm. These bound proteins were imported into the STRING database (STRING 11.0) to perform network interaction analysis of protein-protein relationships. Interestingly, all poly I:C-bound proteins except for anp32e form a cluster, suggesting that poly I:C-bound proteins are located in a network.<br>

为鉴定鱼类中与聚肌胞苷酸（poly I:C）结合的靶标蛋白，本研究通过匀浆斑马鱼进行样品分离。采用树脂固定化聚肌胞苷酸（poly I:C）捕获细菌蛋白提取物中的靶蛋白。上述结合蛋白经十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（SDS-PAGE）分离后，通过液相色谱-串联质谱（LC-MS/MS）完成鉴定。共计鉴定得到27种蛋白，上述结果表明至少存在27种蛋白可与聚肌胞苷酸（poly I:C）结合。随后，本研究采用基因本体（GO）功能富集分析对这些聚肌胞苷酸结合蛋白进行解析。在细胞组分富集分析中，这些蛋白被归类为细胞质、质膜、细胞骨架、细胞外区域、肌钙蛋白复合物、血红蛋白复合物、胞质大型核糖体亚基以及ATP合酶复合物。在分子功能富集分析中，这些蛋白的功能涵盖氧结合、ATP结合、钙离子结合、肌动蛋白丝结合、磷脂结合、泛素-蛋白转移酶活性、激酶活性、氧化还原酶活性、组蛋白结合、信号受体复合物衔接子活性、溶菌酶活性、蛋白质二硫键还原酶活性以及核糖体结构组分。在生物过程富集分析中，这些蛋白参与泛素依赖性蛋白分解代谢过程、氧运输、肌肉收缩、胆固醇逆向转运、水解酶活性、肌动蛋白丝组织、胞质翻译延伸、线粒体融合调控、细胞凋亡过程调控、胞质核糖体组装、质子动力势驱动的ATP合成、肽基脯氨酸羟化生成4-羟基-L-脯氨酸、G蛋白偶联受体信号通路以及结构分子活性。综上，这些聚肌胞苷酸结合蛋白覆盖细胞活动的诸多维度。本研究进一步采用STRING软件对这些聚肌胞苷酸结合蛋白的预测蛋白质相互作用（PPI）网络进行分析，并通过马尔可夫聚类算法（MCL）完成聚类。将这些结合蛋白导入STRING数据库（STRING 11.0）以开展蛋白质间相互作用关系的网络分析。值得注意的是，除anp32e外，所有聚肌胞苷酸结合蛋白均形成一个独立聚类簇，表明聚肌胞苷酸结合蛋白构成了一个相互作用网络。