IN SILICO COMPARATIVE STUDY OF PDS, ZDS, ZISO, AND CRTISO GENES INVOLVED IN CAROTENOID BIOSYNTHESIS OF TOMATO (SOLANUM LYCOPERSICUM), CARROT (DAUCUS CAROTA), AND BANANA (MUSA ACUMINATA)

• Main Author: Salima, Hasna
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/65966
• Institution: Institut Teknologi Bandung

Provitamin A carotenoids (?- and ? -carotene) are important compounds needed for various body functions. Tomatoes and carrots are the examples of vegetables with high levels of provitamin A carotenoids (?-carotene), but tend to be low in macronutrients. In contrast, bananas have a low content of provitamin A carotenoids, but are rich in macronutrients (carbohydrates and protein). This makes the biofortification of provitamin A carotenoids in bananas attractive because bananas also have high production and consumption rates, especially in Africa and Southeast Asia. However, research on the genes and proteins encoding enzymes involved in the desaturation process, namely phytoene desaturase (PDS) and zeta carotene desaturase (ZDS), as well as enzymes involved in the isomerization process, namely zeta carotene isomerase (ZISO) and carotenoid isomerase (CRTISO) in the biosynthesis of carotenoids in tomatoes (Solanum lycopersicum), carrots (Daucus carota), and bananas (Musa acuminata) has not been widely carried out. This study aimed to (i) identify the structural characteristics of PDS, ZDS, ZISO, and CRTISO genes and proteins in tomatoes, carrots, and bananas; (ii) and to search for PDS, ZDS, ZISO, and CRTISO protein candidates in tomatoes and carrots for biofortification of provitamin A carotenoids in bananas. The gene sequences were obtained from KEGG and then BLASTN was performed on Sol Genomics Network for tomatoes, NCBI for carrots, and Banana Genome Hub for bananas. Gene structure characterization included identification of the presence and number of exon-introns, gene length, analysis of the similarity percentage of paralog gene sequences with pairwise sequence alignment, and analysis of cis-acting regulatory elements (CAREs). Protein sequences were used to identify domains and motifs using the CD-Search Tool, MEME-Suites, and InterPro and multiple sequence alignment was performed to compare the reference motif with the consensus motif. Prediction of the secondary structure of beta-strands on PDS, ZDS, and CRTISO proteins was also carried out. Analysis of the similarity percentage of the carrot ZDS and the banana ZISO paralog gene, respectively, were 88.2% and 83.9% identical. The structural characteristics of the four genes in the three species differ in terms of the distribution of exons and introns, but the number of exons and introns the majority are the same between the same types of genes. The structure of the PDS and ZDS genes in bananas as well as the ZISO and CRTISO genes in tomatoes tend to be longer. The light CAREs response had the highest frequency in all four genes in the three species. An important motif for PDS, ZDS, and CRTISO proteins is the dinucleotide binding motif, while an important motif for ZISO proteins is the NnrU domain. Additional beta-strand secondary structures were found in the N-terminal protein of PDS and CRTISO of tomatoes that could affect the activity of dinucleotide binding motifs binding to their cofactors but were not found in carrots, which are organisms high in ?-carotene. Based on that, the three organisms compared in this study have not found potential protein candidates for biofortification of provitamin A carotenoids in bananas.