Comparative and phylogenetic analysis of RuBisCO large subunit (rbcL) proteins in some Sideritis L. (Lamiaceae) species: A bioinformatic approach

Abstract

The large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) protein, which plays an important role in the photosynthesis reaction, are encoded by the chloroplast genome. Sideritis L., a medical and aromatic plant group, belongs to Lamiaceae family. In this study, we performed sequence, physicochemical, phylogenetic and three-dimensional (3D) bioinformatic analyses of RuBisCO large subunit (rbcL) proteins in the Sideritis ssp. using various bioinformatics tools. Physicochemical analyzes were performed by ExPASy - ProtParam. The putative phosphorylation sites of the rbcL proteins were determined by NetPhos 2.0 and NetPhos 3.1. Phylogenetic analyses were performed with the MEGA 6.0 software. To estimate 3D protein structures, PyMol program was used. At the end of the study, it was found that the amino acid number of stilbene synthase proteins ranged between 171 and 456, molecular weight ranged between 19002.67 and 50420.44 Da, instability index ranged between 27.30 to 40.70 and GRAVY values ranged between -0.394 to -0.226. While the highest average amino acid rate in the rbcL proteins was Gly (10.00%), the lowest amino acid ratio (1.4%) was determined as Trp. In phylogenetic analyses performed using protein sequences, maximum likelihood (ML) tree consisted of 2 large clades. Pairwise distance analysis based on Sideritis species? rbcL protein sequences was performed using MEGA 6.0. The lowest pairwise distance was 0.000, while the highest pairwise distance was 0.024. When the estimated 3D structures of the proteins were examined, the Gly residue, which plays an important role in the structure and function of the proteins, was detected as the least in S. libanotica subsp. kurdica species while it was the most abundant residue in S. cretica subsp. spicata. The results of our study provide insights into fundamental characteristics of rbcL proteins in Sideritis taxa.