Computational approaches for prediction of protein-protein interaction between Foot-and-mouth disease virus and Sus scrofa based on RNA-Seq
2
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Foot-and-Mouth Disease (FMD) is a highly contagious trans-boundary viral disease caused by FMD vi-rus, which causes huge economic losses. FMDV infects cloven hoofed (two-toed) mammals such as cat-tle, sheep, goats, pigs and various wildlife species. To control the FMDV, it is necessary to understand the life cycle and the pathogenesis of FMDV in host. Especially, the protein-protein interaction between FMDV and host will help to understand the survival cycle of viruses in host cell and establish new therapeutic strategies. However, the computational approach for protein-protein interaction between FMDV and pig hosts have not been applied to studies of the onset mechanism of FMDV. In the present work, we have performed the prediction of the pig’s proteins which interact with FMDV based on RNA-Seq data, protein sequence, and structure information. After identifying the virus-host interaction, we looked for meaningful pathways and anticipated changes in the host caused by infection with FMDV. A total of 78 proteins of pig were predicted as interacting with FMDV. The 156 interactions include 94 interactions predicted by sequence-based method and the 62 interactions predicted by struc-ture-based method using domain information. The protein interaction network contained integrin as well as STYK1, VTCN1, IDO1, CDH3, SLA-DQB1, FER, and FGFR2 which were related to the up-regu-lation of inflammation and the down-regulation of cell adhesion and host defense systems such as mac-rophage and leukocytes. These results provide clues to the knowledge and mechanism of how FMDV affects the host cell.
Abstract
Foot-and-Mouth Disease (FMD) is a highly contagious trans-boundary viral disease caused by FMD vi-rus, which causes huge economic losses. FMDV infects cloven hoofed (two-toed) mammals such as cat-tle, sheep, goats, pigs and various wildlife species. To control the FMDV, it is necessary to understand the life cycle and the pathogenesis of FMDV in host. Especially, the protein-protein interaction between FMDV and host will help to understand the survival cycle of viruses in host cell and establish new therapeutic strategies. However, the computational approach for protein-protein interaction between FMDV and pig hosts have not been applied to studies of the onset mechanism of FMDV. In the present work, we have performed the prediction of the pig’s proteins which interact with FMDV based on RNA-Seq data, protein sequence, and structure information. After identifying the virus-host interaction, we looked for meaningful pathways and anticipated changes in the host caused by infection with FMDV. A total of 78 proteins of pig were predicted as interacting with FMDV. The 156 interactions include 94 interactions predicted by sequence-based method and the 62 interactions predicted by struc-ture-based method using domain information. The protein interaction network contained integrin as well as STYK1, VTCN1, IDO1, CDH3, SLA-DQB1, FER, and FGFR2 which were related to the up-regu-lation of inflammation and the down-regulation of cell adhesion and host defense systems such as mac-rophage and leukocytes. These results provide clues to the knowledge and mechanism of how FMDV affects the host cell.
참고문헌 (28)
- S Alexandersen, "The Pathogenesis and Diagnosis of Foot-and-Mouth Disease", Journal of Comparative Pathology, 129(1), pp.1~36 (2003), Elsevier BV[DOI]
- Baxt B., "The effect of peptides containing the arginine-glycine-aspartic acid sequence on the adsorption of foot-and-mouth disease virus to tissue culture cells", Virus genes, 4(1), pp.73~83 (1990)
- Bindea G, "ClueGO : a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks", Bioinformatics(Oxford, England), 25(8), pp.1091~1093 (2009)[DOI]
- Grzegorz M Boratyn, "Domain enhanced lookup time accelerated BLAST", Biology Direct, 7(1), pp.12~ (2012), Springer Science and Business Media LLC[DOI]
- Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View, "UniProtKB", pp.2016, Boutet E
- L. S. Christensen, "Analysis of the epidemiological dynamics during the 1982-1983 epidemic of foot-and-mouth disease in Denmark based on molecular high-resolution strain identification", Journal of General Virology, 86(9), pp.2577~2584 (2005), Microbiology Society[DOI]
- Helen Cook, "Viruses.STRING: A Virus-Host Protein-Protein Interaction Database", Viruses, 10(10), pp.519~ (2018), MDPI AG[DOI]
- Dobin A, "STAR : ultrafast universal RNA-seq aligner", Bioinformatics(Oxford, England), 29(1), pp.15~21 (2013)[DOI]
- Fox NK, "SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures", Nucleic Acids Research, 42(D1), pp.D304~D309 (2014)[DOI]
- Franzosa EA., "Structural principles within the human- virus protein-protein interaction network", Proceedings of the National Academy of Sciences (2011)
- Yuan Gao, "Biological function of Foot-and-mouth disease virus non-structural proteins and non-coding elements", Virology Journal, 13(1) (2016), Springer Science and Business Media LLC[DOI]
- D. P. Gladue, "Foot-and-Mouth Disease Virus Nonstructural Protein 2C Interacts with Beclin1, Modulating Virus Replication", Journal of Virology, 86(22), pp.12080~12090 (2012), American Society for Microbiology[DOI]
- Shi-Chong Han, "Productive Entry of Foot-and-Mouth Disease Virus via Macropinocytosis Independent of Phosphatidylinositol 3-Kinase", Scientific Reports, 6(1) (2016), Springer Science and Business Media LLC[DOI]
- Zohar Itzhaki, "Domain-Domain Interactions Underlying Herpesvirus-Human Protein-Protein Interaction Networks", PLoS ONE, 6(7), pp.e21724~ (2011), Public Library of Science (PLoS)[DOI]
- T. Jackson, "Integrin v 8 Functions as a Receptor for Foot-and-Mouth Disease Virus: Role of the -Chain Cytodomain in Integrin-Mediated Infection", Journal of Virology, 78(9), pp.4533~4540 (2004), American Society for Microbiology[DOI]
- Sandra N. Lester, "Toll-Like Receptors in Antiviral Innate Immunity", Journal of Molecular Biology, 426(6), pp.1246~1264 (2014), Elsevier BV[DOI]
- Liao Y, "featureCounts : an efficient general purpose program for assigning sequence reads to genomic features", Bioinformatics, 30(7), pp.923~930 (2014)[DOI]
- Neff S, "Foot-and-mouth disease virus virulent for cattle utilizes the integrin alpha(v)beta3 as its receptor", Journal of virology, 72(5), pp.3587~3594 (1998)
- Jong Park, "Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast11Edited by J. Karn", Journal of Molecular Biology, 307(3), pp.929~938 (2001), Elsevier BV[DOI]
- Muhammad Farooq Rai, "Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears", Journal of Orthopaedic Research (2017), Wiley[DOI]
- Robinson MD, "edgeR : a Bioconductor package for differential expression analysis of digital gene expression data", Bioinformatics(Oxford, England), 26(1), pp.139~140 (2010)[DOI]
- Miguel Rodríguez Pulido, "Molecular Mechanisms of Foot-and-Mouth Disease Virus Targeting the Host Antiviral Response", Frontiers in Cellular and Infection Microbiology, 7 (2017), Frontiers Media SA[DOI]
- Shen J, "Predicting protein-protein interactions based only on sequences information", Proceedings of the National Academy of Sciences (2007)
- A. J. Walhout, "Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development", Science, 287(5450), pp.116~122 (2000), American Association for the Advancement of Science (AAAS)[DOI]
- D. Wang, "The Leader Proteinase of Foot-and-Mouth Disease Virus Negatively Regulates the Type I Interferon Pathway by Acting as a Viral Deubiquitinase", Journal of Virology, 85(8), pp.3758~3766 (2011), American Society for Microbiology[DOI]
- Zichen Wang, "An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study", F1000Research, 5, pp.1574~ (2016), F1000 Research Ltd[DOI]
- H. Yu, "Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs", Genome Research, 14(6), pp.1107~1118 (2004), Cold Spring Harbor Laboratory[DOI]
- Tianliang Zhang, "Transcript Profiling Identifies Early Response Genes against FMDV Infection in PK-15 Cells", Viruses, 10(7), pp.364~ (2018), MDPI AG[DOI]