Proteome-scale investigation of zinc-binding proteins of bread wheat

Abstract Zinc (Zn) is an essential micronutrient participating in many cellular functions and performs structural and regulatory roles in wheat. Bread wheat, one of the most widely cultivated and consumed crops worldwide, has a relatively low zinc concentration. This study focuses on the recognition of zinc-binding proteins (ZBPs) across the proteome of bread wheat ( Triticum aestivum L.) through a systematic bioinformatic analysis. The extensive size and complex nature of the wheat proteome on profiling with BLASTp produced a high volume of redundant proteins. Further, filtering was done based on metal-binding motifs of proteins by employing the MeBiPred tool, producing an output of 2,719 putative ZBPs. The putative ZBPs were modeled using AlphaFold3, and 662 high-confidence ZBPs were shortlisted for downstream analysis. These putative proteins were predicted to be predominantly present in the nucleus, followed by the chloroplast and cytoplasm. The functional analysis revealed the prevalence of domains such as peroxidase, carbonic anhydrase, and transcription regulators like C2H2 zinc finger, indicating their role in stress responses, mediating cellular signalling, and regulating nucleic acid biosynthesis. Their involvement in metabolic processes and pathways defines their importance in maintaining homeostasis, regulating gene expression, maintaining structural integrity, and balancing oxidative stress. ZBPs performing similar functions were clustered in a protein–protein interactions , revealing the network of hub genes and the presence of uncharacterised proteins regulating the core metabolic processes in plants. Identification of these uncharacterised proteins was done by cytoHubba and MCODE providing us an edge to identify ZBPs that could serve as potential biomarkers for crop biofortification programs.