Subtractive Genome mining in Xanthomonas citri pv. Citri strain 306 for identifying novel drug target proteins coupled with in-depth protein-protein interaction and coevolution analysis - A leap towards prospective drug design

Citrus canker (CC) poses a serious threat to a highly significant citrus fruit crop, this disease caused by one of the most destructive bacterial plant pathogens Xanthomonas citri pv. citri. Bacterial plant diseases cause substantial global losses in crop production. Reducing crop yield losses is necessary to meet growing global food demands with a rising population. High rates of antibiotic resistance to conventional pesticides and antibiotics among Xanthomonas citri pv . citri (XCC) strains the effectiveness of current control methods is diminishing, have rendered treatment management more challenging and highlighted the need for novel therapeutic targets or new approaches to combat the rising antimicrobial resistance trend. Utilizing OMICS data offers an appealing alternative to experimental methods, propelling drug discovery and reducing the risk of later-stage drug failures. Using an innovative hierarchical computational method, the goal of this present study was to identify and characterize potential drug targets against the pathogen XCC strain 306. The study involved retrieving the XAC proteome from the UniProt database, eliminating paralogous proteins using CD-HIT (80% identity cutoff), and selecting nonhomologous proteins through BLASTp (e-value < 0.005). Essential proteins were identified using BLAST against the DEG (e-value cutoff 0.00001). Subsequent analyses included metabolic pathway assessment, subcellular localization prediction, and druggability analysis. Protein network analysis, coevolution analysis (CoeViz server), protein active site identification (CastP 3.0), and centrality betweenness graph plotting (ProsNex) were performed. In conclusion, this study identified eight drug targets (GlmU, CheA, RmlD, GspE, FleQ, RpoN, Shk, SecB), highlighting RpoN, FleQ, and SecB as unprecedented targets for XCC. These findings may contribute to the development of novel antimicrobial agents in the future that can efficiently control citrus canker disease.