Journal of Data Mining in Genomics & Proteomics

Abstract

Structural, Functional Annotation of Complete Protein Coding Regions of TYLCV and Molecular Docking of Rep and Ren proteins with Resistance Genes Ty-2, Ty-5, and Yy-6 to Module Precise Molecular Auditing of Pathogen

Muhammad Tayyab, Sarmad Frogh Arshad*, Abdul Malik, Muhammad Usman, Asif Saleem, Imran Ahmad Khan, Hasan Junaid Arshad, Asma Shah Rukh, Muhammad Tahir and Qasim Ali Ghauri

Tomato Yellow Leaf Curl Virus (TYLCV), a single-stranded DNA begomovirus, belongs to the family Geminiviridae, which encodes six Open Reading Frames (ORFs). Host pathogen interaction studies revealed different resistance genes (Ty-2, Ty-5, and Ty-6) whose binding affinities and interaction patterns are still unclear against TYLCV. It is a dire need to understand the ORFs of TYLCV at the computational level to get insight into their electrostatic interaction, hydrogen bonding patterns, and binding affinities with resistance genes. In the recent study, comprehensive proteomic analyses of all encoded regions of TYLCV were performed, and the results revealed that C1 (Rep) protein was present at 30.4% in the nucleus, 34.8% in the mitochondria, and 26.1% in the cytoplasm. The 65.2% area of the mitochondria, with a 34.8% g area of the nucleus, was occupied by the C3 (Ren) factor, while the C4 encoded region showed the highest localization percentage in the mitochondria, which was 78.3% among all encoded factors. Apart from localization, the C3 (Ren) factor has a 7.94 isoelectric Pi, -0.124 hydropathicity rate, and a 28.74 instability index, indicating its stable and hydrophilic nature. Moreover, molecular docking analyses depicted that the C3 (Ren) protein had a binding affinity of -6.3 kcal/mol with the Ty-5 gene, which was the highest of all interactions, and C1 (Rep) interacted with the Ty-5 gene with a binding affinity of -6.0 kcal/mol, which encodes for replication in the host. In conclusion, results showed that C3 (Ren) was more stable and had greater binding affinity with the Ty-2, Ty-5, and Ty-6 genes in comparison to the other ORFs of TYLCV. In the future, results will be helpful in precise genome editing and hybrid peptide development to cure the infection of TYLCV.

Published Date: 2025-09-23; Received Date: 2024-10-23