Genome-wide identification and analysis of RuBisCO large subunit proteins in Morus L. (Moraceae) species

Abstract

In this study, we performed sequence, physicochemical, phylogenetic, and comparative 3D (three-dimensional) analyses of RuBisCO large subunit proteins of the Morus species using various bioinformatics tools. The sequence lengths of the RuBisCO proteins varied between 140 and 475 amino acids with molecular weights (MW) ranging from 15463.40 to 52667.95 Da. The most acidic protein sequences were in M. australis, M. rotundiloba, M. serrata, and M. cathayana (pI=4.77). The extinction coefficients of the proteins at 280 nm ranged from 21430 to 69830 M-1 cm-1 , the instability index (II) values ranged from 26.06 to 42.17, and the GRAVY values ranged from-0.355 to-0.215. The most abundant amino acid of RuBisCO proteins was Gly (9.5%) while the least abundant ones were Cys and Trp (1.5%). Based on the phylogenetic analysis, the tree constructed using RuBisCO proteins is composed of three main clades. A RAMPAGE analysis revealed that 96.1%-98.5% of residues were located in the favored region in RuBisCO proteins. To predict the three dimensional (3D) structures of the RuBisCO proteins PyMOL was used. The highest number of Gly residues was detected in M.mongolica, M. indica, M.notabilis, M. alba var. atropurpurea and M. alba var. multicaulis, while the least Gly residues were detected in M. australis, M.rotundiloba, M. serrata and M.cathayana. The results of our study provide insights into fundamental characteristic of RuBisCO proteins in Morus species.