Computational analysis of 16D10 effector peptides from root-knot nematodes and their interaction with Mi resistance (R) protein through molecular docking

Abstract

Plant-parasitic nematodes, especially root-knot nematodes (RKNs), pose significant threats to global agriculture, affecting both the quantity and quality of crop yields. Central to the parasitism strategy of RKNs is the deployment of effector proteins, such as the 16D10 peptide, which interact with host plant resistance mechanisms. This study focuses on the computational analysis and molecular docking of 16D10 effector peptides derived from major RKN species (M. incognita, M. arenaria, M. hapla, M. javanica, and M. chitwoodi) to explore their interaction with the Mi resistance protein in tomatoes. Initial bioinformatics assessments included sequence retrieval, multiple sequence alignment, and phylogenetic analysis, utilizing tools such as CLUSTALW and the MEME Suite. Notably, our phylogenetic analysis revealed a close evolutionary relationship between M. incognita and M. chitwoodi, contrasting with other RKN species based on both DNA and protein data. Subsequent, in silico 3D modeling and docking studies, conducted using Chem-Sketch and MOE software, provided insights into the structural basis of the interaction between 16D10 peptides and the Mi protein. Our findings indicate that these interactions could play a crucial role in the modulation of plant defense mechanisms, potentially leading to effector-triggered susceptibility (ETS). This study not only enhances our understanding of nematode-host interactions but also aids in the development of novel strategies for managing RKN infections in economically important crops.