Abstract
BackgroundThe influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen.ResultsIn this study, a data mining approach was employed to extract influenza-human Protein-Protein interactions (PPI) from VirusMentha,Virus MINT, IntAct, and Pfam databases, to mine motif-domain interactions (MDIs) stored as Regular Expressions (RegExp) in 3DID database. A total of 107 RegExp related to human MDIs were searched on 51,242 protein fragments from H1N1, H1N2, H2N2, H3N2 and H5N1 strains obtained from Virus Variation database. A total 46 MDIs were frequently mapped on the IAV proteins and shared between the different strains. IAV kept host-like MDIs that were associated with the virus survival, which could be related to essential biological process such as microtubule-based processes, regulation of cell cycle check point, regulation of replication and transcription of DNA, etc. in human cells. The amino acid motifs were searched for matches in the immune epitope database and it was found that some motifs are part of experimentally determined epitopes on IAV, implying that such interactions exist.ConclusionThe directed data-mining method employed could be used to identify functional motifs in other viruses for envisioning new therapies.
Highlights
The influenza A virus (IAV) is a constant threat for humans worldwide
The study by Shapira et al, [3] provides three thought-provoking observations: 1) the influenza virus-virus protein interactions are highly interconnected, suggesting as feature related to the formation of a compact virion, 2) the influenza virus proteins interact with a higher number of human proteins than the human to human interactions, as a viral advantage to increase the heterogeneity of activity per protein, and 3) the human proteins contacted a greater number of influenza proteins, suggesting the García-Pérez et al BMC Bioinformatics (2018) 19:238 possible presence of multiprotein complexes of virus-host interactions
Global comparative analysis of the mapped motifs on IAV viral proteins and strains From 1093 interactions of the mined IAV-human network (Additional file 1: Table S1) the human sequences with domain information were used to mine the 3DID database. With this information a total of 110 Regular Expressions (RegExp) (Additional file 1: Table S2) associated to human motif-domain interactions (MDIs) were retrieved from 3DID. Those RegExp were searched on the IAV viral proteins from five strains to map an amino acid motif related to a human MDIs
Summary
The influenza A virus (IAV) is a constant threat for humans worldwide. The Influenza A virus (IAV) is considered an infectious threat worldwide for humans [1]. Studies on protein-protein interactions of IAV gene products have provided some interesting information in the context of virus-host interaction. Another study, using a statistical system biology approach, revealed that the inflammatory protein-protein interaction network for IAV is distinct to protein-protein interactions for normal processes (in human body). This information could be crucial for the understanding of the mechanism of pathogenesis to prevent and control the complications related to the infection [4]
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