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Analysis of host protein interactions in plant viruses: an in silico study using Sesbania mosaic virus

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Abstract

The dynamics of interactions of viral proteins with their host are pivotal in establishing a successful infection and ensuring systemic spread. To uncover these, an in silico analysis of the interactions between the coat protein (CP) of Sesbania mosaic virus (SeMV), a group IV virus with single-stranded positive-sense RNA genome was carried out with the known crystal structures of proteins belonging to the Fabaceae family, which is its natural host. SeMV is an isometric plant virus which infects Sesbania grandiflora, a member of Fabaceae, and causes mosaic symptoms. Earlier results have indicated that the assembly and disassembly events of SeMV favor the formation of CP dimers. Hence, the ability and strength of interactions of CP dimer with the host proteins were assessed using in silico protein–protein docking approaches. A set of 61 unique crystal structures of native proteins belonging to Fabaceae were downloaded from the Protein Data Bank (PDB) and docked with the CP dimer of SeMV. From the docking scores and interaction analysis, the host proteins were ranked according to their strength and significance of interactions with the CP dimers. The leads that were identified present themselves as strong candidates for developing antivirals against not only SeMV but also other related viruses that infect Fabaceae. The study is a prototype to understand host protein interactions in viruses and hosts.

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Acknowledgements

SV acknowledges the support of SERB for funding the study (ECR/2016/000242). The authors thank Prof. Vijay S. Reddy from TSRI, La Jolla for his critical comments.

Funding

Supported by DST-SERB ECR/2016/000242.

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Authors and Affiliations

  1. Department of Biotechnology, Amity University Haryana, Gurgaon, 122413, India

    Mariya Rashid & Shubham Mittal

  2. Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur, 522510, India

    Sangita Venkataraman

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  1. Mariya Rashid
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  2. Shubham Mittal
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  3. Sangita Venkataraman
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SV was involved in conceptualization, data analysis and manuscript preparation. MR and SM were involved in data generation, analysis and manuscript writing.

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Correspondence to Sangita Venkataraman.

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Rashid, M., Mittal, S. & Venkataraman, S. Analysis of host protein interactions in plant viruses: an in silico study using Sesbania mosaic virus. Virus Genes 56, 756–766 (2020). https://doi.org/10.1007/s11262-020-01794-w

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  • DOI: https://doi.org/10.1007/s11262-020-01794-w

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