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In silico prediction and validations of domains involved in gossypium hirsutum SnRK1 protein interaction with cotton leaf curl multan betasatellite encoded βC1

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Kamal, Hira, Minhas, Fayyaz ul Amir Afsar, Farooq, Muhammad, Tripathi, Diwaker, Hamza, Muhammad, Mustafa, Roma, Khan, Muhammad Zuhaib, Mansoor, Shahid, Pappu, Hanu R. and Amin, Imran (2019) In silico prediction and validations of domains involved in gossypium hirsutum SnRK1 protein interaction with cotton leaf curl multan betasatellite encoded βC1. Frontiers in Plant Science, 10 . 656. doi:10.3389/fpls.2019.00656

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Official URL: http://dx.doi.org/10.3389/fpls.2019.00656

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Abstract

Cotton leaf curl disease (CLCuD) caused by viruses of genus Begomovirus is a major constraint to cotton (Gossypium hirsutum) production in many cotton-growing regions of the world. Symptoms of the disease are caused by Cotton leaf curl Multan betasatellite (CLCuMB) that encodes a pathogenicity determinant protein, βC1. Here, we report the identification of interacting regions in βC1 protein by using computational approaches including sequence recognition, and binding site and interface prediction methods. We show the domain-level interactions based on the structural analysis of G. hirsutum SnRK1 protein and its domains with CLCuMB-βC1. To verify and validate the in silico predictions, three different experimental approaches, yeast two hybrid, bimolecular fluorescence complementation and pull down assay were used. Our results showed that ubiquitin-associated domain (UBA) and autoinhibitory sequence (AIS) domains of G. hirsutum-encoded SnRK1 are involved in CLCuMB-βC1 interaction. This is the first comprehensive investigation that combined in silico interaction prediction followed by experimental validation of interaction between CLCuMB-βC1 and a host protein. We demonstrated that data from computational biology could provide binding site information between CLCuD-associated viruses/satellites and new hosts that lack known binding site information for protein–protein interaction studies. Implications of these findings are discussed.

Item Type: Journal Article
Subjects: Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software
Q Science > QH Natural history > QH301 Biology
Q Science > QK Botany
Divisions: Faculty of Science > Computer Science
Library of Congress Subject Headings (LCSH): Yeast two-hybrid assay, Cotton -- Viruses, Plant proteins -- Analysis, Geminiviridae
Journal or Publication Title: Frontiers in Plant Science
Publisher: Frontiers Media S.A.
ISSN: 1664-462X
Official Date: 28 May 2019
Dates:
DateEvent
28 May 2019Published
1 May 2019Accepted
Date of first compliant deposit: 4 November 2019
Volume: 10
Article Number: 656
DOI: 10.3389/fpls.2019.00656
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
In silico analysis and experimental validation of host-pathogen protein interactions and interfaces; 6085Higher Education Commission, Pakistanhttp://dx.doi.org/10.13039/501100004681

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