Deciphering Dark Proteome of Grapevine Geminivirus: Molecular Insights and Evolutionary Tactics of a Rising Viral Threat in Grapevine and Global Agriculture

Geminiviruses are the major group of plant viruses that infect major cash crops leading to considerable economic loss. Among them, grapevine geminivirus A (GVGV) under the genus Maldovirus poses a rising threat to agriculture, particularly grapevine species. The genome of GVGV is small, single-stranded DNA of about 2.9 kb in size. The genome analysis revealed 18 ORFs, encompassing 6 structural proteins and 12 non-structural proteins. The key structural proteins such as coat protein (CP), replication-associated protein (Rep/C1), and transcriptional activator protein (TrAP) play critical roles in viral replication, infection, and host manipulation, enabling the virus to evade plant immune responses. The phylogenetic analysis of the structural and non-structural proteins reveals that GVGV exhibits potential for recombination and molecular evolution. The proteins have a close evolutionary relationship with a wide range of hosts such as different families of viruses, bacteria, reptiles, plants, animals, and humans. The presence of the orthologue’s protein delineates the evolutionary relationship and their ability to infect a wide range of hosts. Further, the elucidation of intrinsically disordered regions (IDRs) in the GVGV genome highlights their structural flexibility, which facilitates interaction with host factors and enhances viral adaptability. The multifunctional nature of these viral proteins, especially TrAP and C4, allows GVGV to suppress host defenses, manipulate gene expression, and facilitate virus movement within the plant. IDR regions serve as mutational hotspots and antigenic sites, contributing to immune evasion and viral evolution. From the protein-protein interaction analysis, it was observed that key residues (LYS256, HIS278, and TYR298) in the IDR of Rep have shown interaction with RBR. Thus, the study emphasizes the importance of molecular characterization of GVGV to understand the viral-host interactions. Targeting the critical proteins and IDRs will offer potential avenues for the development of antiviral agents and resistance in plants. Future research focuses on innovative control methods that can be involved in the mitigation of viral impacts in cash crops mainly grapevine and maintain sustainability in agriculture.