Bioinformatic study of copper-associated proteins of bread wheat

Bread wheat is the staple food, but the concentration of mineral micronutrient, Copper (Cu) is relatively low with limited bioavailability. This study investigates the various copper-associated proteins in bread wheat using high-throughput systematic bioinformatics approaches. The wheat proteome was investigated for putative copper-associated proteins, and 47 Copper-binding proteins (CBPs) and 24 Copper transporter proteins (CTPs) were shortlisted. Out of these proteins, 11 were reported as common proteins and predicted to perform both functions. The identified 60 putative proteins showed diverse coordination geometry when bound to Cuprous (Cu⁺) and Cupric (Cu²⁺) ions. The Cysteine, Histidine, Glutamate, and Aspartate (CHED) amino acid residues were mostly found in the binding pockets of the proteins bound to copper. Functional classification and subcellular localisation of these proteins were also performed using sequence-based and annotation-based tools. Proteins were segregated based on their family, subfamily, functional classes and gene ontology (GO) terms, and a comprehensive report was prepared. A network analysis of the shortlisted proteins was also done, and network clusters were made using annotation tools. This report highlights the diverse roles of copper-associated proteins in the proper functioning of the plant and explains their importance in the major functions performed by the plant cell, like energy production, photosynthesis, plant growth and development, and maintaining homeostasis.