Genome-wide identification and comparative structural analysis of RuBisCo proteins in the asteraceae

• Published in: Horticulture, environment and biotechnology environment and biotechnology, 2016-08, Vol.57 (4), p.404-414
• Main Authors: Avci, Murat Kemal, Tezcan, Erdem, Sevindik, Emre
• Format: Article
• Language: English
• Subjects: Agriculture; Alignment; Aliphatic compounds; Amino acids; Biomedical and Life Sciences; Dimensional analysis; Enzymes; Genomes; Gravy; In vitro methods and tests; Life Sciences; Nucleotide sequence; Ornamental plants; Photosynthesis; Phylogenetics; Phylogeny; Plant Breeding/Biotechnology; Plant Ecology; Plant Physiology; Plants (botany); Proteins; Research Report; Residues; Ribulose-1,5-bisphosphate; Ribulose-bisphosphate carboxylase; Species extinction; Stability; Structural analysis
• ISSN: 2211-3452; 2211-3460
• DOI: 10.1007/s13580-016-0010-3

Asteraceae, the largest known plant family in the world, contains economically important species including ornamental plants. The most abundant enzyme on Earth, Ribulose-1,5-bisphosphate (RuBisCo), catalyzes the first step of carbon assimilation in photosynthesis. In this study, we conducted sequence, physicochemical, phylogenetic, and three-dimensional comparative analyses of 22 RuBisCo proteins in the Asteraceae using various bioinformatic tools. The alignment results showed that all residues corresponding to the region between 48-179 amino acids were conserved in all species, except for just seven residues: G79, I80, S88, F90, F93, I135, and S136. The sequence lengths of the RuBisCo large subunits were between 163 and 477 amino acids, with an average length of 255 amino acids. Their molecular weights (Mw) ranged from 18341.8 to 52895.1 Da, with an average Mw of 26294.5 Da. We found that the most abundant amino acid residue was Gly, which comprised 9.88% of these RuBisCo proteins. Ala (8.17%) and Leu (8.53%) were also both abundant. The extinction coefficient of the RuBisCo proteins at 280 nm ranged from 27515 to 69830 M-1 cm-1. The instability index values ranged from 24.41 to 40.65, and only one protein (from Gymnarrhena micrantha) was unstable in vitro. The aliphatic index values ranged from 72.56 to 81.13, while the GRAVY values ranged from -0.394 to -0.179. A total of ten motifs were identified in the sequences of the RuBisCo proteins. Phylogenetic analysis revealed that the 22 RuBisCo proteins formed two main clades. A RAMPAGE analysis revealed that 95.0-98.4% of residues were located in the favored region in 22 RuBisCo proteins. Sequence alignment and 3D analysis revealed that a catalytically important Lys residue was conserved among all the RuBisCo enzymes of Asteraceae. The results of this study provide insights into the fundamental characteristics of the RuBisCo proteins of the Asteraceae.