In silico study of legume and legume-type lectins

Abstract

In contemporary biological research, bioinformatics and computational biology are essential fields that can help biologists solve and understand complex biological problems and mechanisms. Indeed, recent advances in DNA sequencing technology have helped us to gain insight into the origin, distribution, and evolution of genes and gene families in living organisms. A large-scale genomic study was conducted to search for putative proteins containing the legume-type lectin domain (LLDP) across kingdoms, followed by comprehensive genomics and phylogenetic analyses. Many homologous sequences of the plant LLDP family were newly identified in bacteria and lower eukaryotes, but far fewer than those found universally in land plants. Analyses of the evolution of LLDP genes across kingdoms revealed that members share a common ancestor suggesting a species-specific divergence and expansion of members of the LLDP family in plants. Detailed investigation of LLDP gene pools in sequenced genomes demonstrates that segmental and tandem duplications are two key factors in the rapid expansion of this family in land plants. Calculation of nucleotide substitution rates shows that purifying selection is likely the main driving force for stabilizing selection and evolution of the soybean LLDP genes. Analysis of soybean LLDP gene expression suggests that duplicate genes tend to differ and diverge regarding expression levels and expression partitioning in different studied tissues and development stages. A gene set enrichment study of soybean LLDPs demonstrated a functional conservation among members towards carbohydrate binding and kinase activity. In addition, molecular modeling and docking studies were also performed on the LLD domain of DORN1 protein, an important plant receptor-like kinase of the LLDP family, leading to the identification and in vitro characterization of its ligand-binding site and key binding residues interacting with an adenosine triphosphate substrate.