Gene sequencing and molecular characterization of phytoene synthase (psy) in sugod-sugod (Momordica cochinchinensis)
2019
Dela Cruz, D.C.DM. | Manohar, A.N.C. | Mateo, J.M.C. | Gardoce, R.C. | Galvez, H.F.
This study reports the gene sequencing of the phytoene synthase (psy) in sugod-sugod (Momordica cochinchinensis) and characterization of its nucleotide and predicted protein sequences. Sugod-sugod, also known as balbas-bakiro and buyok-buyok in some provinces in the Philippines, is known to have higher concentration of lycopene and B-carotene as compared to the primary sources of these carotenoids, tomato and carrot, but is not fully utilized due to the lack of existing studies. The psy gene of sugod-sugod was sequenced based on homology with the psy gene in tomato as the reference gene sequence, carrot, and other crops belonging in the family Cucurbitaceae. Gene-specific primers were designed to amplify through PCR the psy gene sequence. The amplified gene was sequenced and characterized for both the nucleotide and predicted protein sequences. Outputs from multiple sequence alignments of nucleotide and protein sequences were used to generate the phylogenetic relationship and ontology of the psy genes among the gene sequence of sugod-sugod against the gene sequences of tomato, carrots, and other related cucurbits. The orthologous protein sequences, structural analogs, predicted function and molecular structure of the phytoene synthase gene were determined through bioinformatics analysis using BLASTp, TM-Align, and COACH through the I-TASSER server. The gene has a predicted total gene sequence of 1465 base pairs, with its Open Reading Frame found from the 670th to the 1239th base pair. Preliminary structural annotation has also validated its isoprenoid synthase domain and catalytic activity specifically in the carotenoid biosynthesis.
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