Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions
文献类型:期刊论文
作者 | Zhang, Aidi; He, Libo; Wang, Yaping |
刊名 | BMC BIOINFORMATICS |
出版日期 | 2017-03-02 |
卷号 | 18期号:1页码:13 |
ISSN号 | 1471-2105 |
关键词 | Hemorrhagic disease Reovirus Protein-protein interactions Motif Domain GCRV |
DOI | 10.1186/s12859-017-1500-8 |
英文摘要 | Background: Grass carp hemorrhagic disease, caused by grass carp reovirus (GCRV), is the most fatal causative agent in grass carp aquaculture. Protein-protein interactions between virus and host are one avenue through which GCRV can trigger infection and induce disease. Experimental approaches for the detection of host-virus interactome have many inherent limitations, and studies on protein-protein interactions between GCRV and its host remain rare. Results: In this study, based on known motif-domain interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction pair searching strategy. These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. Differentially expressed genes during GCRV infection process were extracted and mapped to our predicted interactome, the overlapped genes displayed different tissue expression distributions on the whole, the overall expression level in intestinal is higher than that of other three tissues, which may suggest that the functions of these genes are more active in intestinal. Function annotation and pathway enrichment analysis revealed that the host targets were largely involved in signaling pathway and immune pathway, such as interferon-gamma signaling pathway, VEGF signaling pathway, EGF receptor signaling pathway, B cell activation, and T cell activation. Conclusions: Although the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. The findings of this work will contribute to the development of system biology for GCRV infectious diseases, and help guide the identification of novel receptors of GCRV in its host. |
WOS关键词 | GRASS CARP REOVIRUS ; CTENOPHARYNGODON-IDELLUS ; PRINCIPLES ; DISEASE ; INFECTION ; SEQUENCE ; CHINA ; GENE ; CYTOSCAPE ; NETWORKS |
资助项目 | Strategic Priority Research Programme of Chinese Academy of Sciences[XDA08030203] ; National Natural Science Foundation of China[31130055] ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology[2014FBZ04] |
WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
语种 | 英语 |
出版者 | BIOMED CENTRAL LTD |
WOS记录号 | WOS:000397507700001 |
资助机构 | Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; 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Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; 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National Natural Science Foundation of China ; National Natural Science Foundation of China ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; 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National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Strategic Priority Research Programme of Chinese Academy of Sciences ; 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Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; Strategic Priority Research Programme of Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology ; Independent project of State Key Laboratory of Freshwater Ecology and Biotechnology |
源URL | [http://ir.ihb.ac.cn/handle/342005/32915] |
专题 | 水生生物研究所_其他_期刊论文 |
通讯作者 | Wang, Yaping |
作者单位 | Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China |
推荐引用方式 GB/T 7714 | Zhang, Aidi,He, Libo,Wang, Yaping. Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions[J]. BMC BIOINFORMATICS,2017,18(1):13. |
APA | Zhang, Aidi,He, Libo,&Wang, Yaping.(2017).Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions.BMC BIOINFORMATICS,18(1),13. |
MLA | Zhang, Aidi,et al."Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions".BMC BIOINFORMATICS 18.1(2017):13. |
入库方式: OAI收割
来源:水生生物研究所
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