In silico prediction of faba bean necrotic yellows virus proteins and their interactions with host protein SnRK1 through expression analysis

Faba bean necrotic yellows virus (FBNYV) is a multipartite nanovirus (family Nanoviridae) that poses a significant threat to legume crops worldwide. Its genome encodes various viral proteins that promote infection, systemic spread, and vector transmission. This study evaluated the interaction dynamics between the sucrose non-fermenting 1-related kinase 1 (SnRK1) and eight key FBNYV proteins using in silico docking analysis. All the viral proteins bound to SnRK1 with notable affinity; however, the nuclear shuttle protein encoded by DNA-N showed the strongest binding affinity to SnRK1, revealing that it may modulate host energy signaling. Alongside the computational results, we performed quantitative reverse transcription-polymerase chain reaction analysis of SnRK1 in faba bean plants inoculated with FBNYV using varying concentrations of the viral DNA-N segment. SnRK1 transcript levels were elevated in infections with higher DNA-N dosage, revealing a host response aimed at curbing viral replication. The expression profiles of key plant defense-related genes (WRKY33, bZIP11, AGO2, ATG8, ATL2, and MKS1) were also assessed. Notably, genes related to stress and immune signaling (such as WRKY33, bZIP11, and ATG8) were induced, whereas the RNA-silencing gene AGO2 was suppressed. These findings improve our understanding of host-virus interactions in faba beans and highlight the dual role of SnRK1 in metabolic regulation and antiviral defense. Overall, this study provides a strong molecular foundation for enhancing resistance to FBNYV. IMPORTANCE: Considering the critical role of SnRK1 in plant stress responses and antiviral defense, this study used in silico approaches to identify FBNYV proteins that interact with SnRK1 and to infer the potential impacts on host immunity. Similar to geminiviruses, nanoviruses are circular DNA viruses that rely on the cellular machinery for replication and spread. Although previous research on the antiviral functions of SnRK1 has predominantly focused on geminivirus infections, the parallels between geminivirus and nanovirus host interactions show that SnRK1 could play a comparable defensive role against nanoviruses like FBNYV. By investigating the interaction of SnRK1 with FBNYV proteins and monitoring related defense gene expression, our work provides insight into how this host kinase may contribute to resistance. Ultimately, understanding this relationship may facilitate the development of virus-resistant faba bean varieties through targeted breeding or biotechnological approaches.