A Multifaceted Computational Analysis of Bacterioruberin Biosynthesis Pathway Proteins in the Underexplored Archaeon Haloarcula japonica TR-1

Bacterioruberin is a rare C50-carotenoid produced by halophilic archaea and possesses therapeutic properties as an antioxidant, anticancer, and antimicrobial agent. The proteins involved in its biosynthesis pathway have been identified, but there are only a few structural and functional data on it, especially in the Haloarcula japonica strain TR-1. To address this, a comprehensive in silico analysis was performed to examine the structure and function of proteins in the underexplored bacterioruberin biosynthesis pathway. Phylogenetic analysis confirmed that all the retrieved proteins belong to the Haloarculaceae family. Sequence-based analysis revealed diverse physicochemical properties. The distribution of proteins was determined using subcellular localization, transmembrane domain, and signal-peptide analyses. The data revealed unique signature motifs, and the proteins were classified into major classes based on their conserved domains and families. Protein-protein interaction analysis revealed potential functional partners. Binding pockets and active residues of these proteins were also identified. Finally, the predicted 3D structures of TR-1 proteins were validated and submitted to the Protein Model DataBase. To our knowledge, this is the first report to characterize the structure and function of BBP proteins on the underexplored yet potential archaeal strain. Our insights provide a foundation for metabolic engineering-based systems approaches for the sustainable production of bacterioruberin.