Dishita Mishra^1,2#, Ranjit Shaw^3,4#, Kishori Lal¹#, Md Zishan Ansari⁵ and Radha Chaube³*

¹School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi- 221005, Uttar Pradesh, India
²Kusuma School of Biological Sciences, IIT Delhi, Hauz Khas, New Delhi-110016, India
³Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
⁴Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai- 400076, India
⁵Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Berhampur760003, Odisha, India

*Corresponding Author: Radha Chaube, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India.
# Equal Contributions.

Received: October 24, 2025; Published: November 13, 2025

Abstract

The interaction between plants and pathogens is a co-evolutionary process. Host plants have innate immunity receptors that recognize pathogen-related effector proteins. Ralstonia solanacearum causes bacterial wilt by secreting effector molecules via the type III secretion system. XopQ protein in this bacterium is recognized by the Roq1 receptor in Solanaceae species. However, the physicochemical mechanism underlying this interaction in Nicotiana rustica is still not completely understood. In this study, we used a computational approach to identify and characterize the interaction between the N. rustica Roq1 and the R. solanacearum XopQ proteins. The primary sequence of Roq1 was predicted using FGENESH and functionally characterized using InterProScan. Physicochemical properties were analyzed using ProtParam. Homology modeling of Roq1 and XopQ was performed using SWISSMODEL, validated by SAVES v6.1, and classified using CATH. Molecular docking was performed using ZDOCK 3.0.2, and interaction hot spots were identified using the KFC Server. Molecular dynamics simulations using WebGro assessed structural stability. A total of 14 residues in Roq1 and 23 residues in XopQ were found to be actively involved in stable protein–protein interactions. The Roq1-XopQ complex exhibited enhanced stability, suggesting conformational changes associated with immune activation. The understanding of Roq1-XopQ interaction can be important in the modification of immune receptors through molecular breeding or genome editing. The identification of conserved interface residues can be useful for the transfer of Roq1-like resistance traits into crops susceptible to bacterial wilt and related diseases. Transgenic expression of Roq1 in crops like tomato and pepper confers strong immunity, minimizing yield losses and reducing pesticide reliance for sustainable agriculture. The in-silico findings reported in this study can be further validated by in vivo studies.

Keywords: Innate Immunity; Type III Secretion System; Physico-chemical Mechanism; Molecular Docking; Protein-Protein Interactions

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Citation

Citation: Radha Chaube., et al. “Computational Structural Modelling, Characterization, and Interaction Analysis of Nicotiana rustica Roq1 and Ralstonia solanacearum XopQ Effector Proteins".Acta Scientific Veterinary Sciences 7.11 (2025): 21-32.

Copyright

Copyright: © 2025 Radha Chaube., et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.