Widodo, Aulia Febrianti (2021) Karakterisasi In-Silico Faktor Transkripsi GbMYB1, GbMYB2, dan GbMYC1 : Regulator Biosintesis Flavonoid pada Tanaman Gynura bicolor DC. Undergraduate thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
Flavonoid adalah salah satu senyawa metabolit sekunder pada tanaman dengan berbagai manfaat. Salah satu tanaman yang berpotensi sebagai sumber flavonoid adalah Gynura bicolor dari famili Asteraceae. Faktor transkripsi GbMYB1, GbMYB2, dan GbMYC1 diketahui berperan penting dalam akumulasi antosianin pada G. bicolor. Namun, belum banyak informasi mengenai studi hubungan kekerabatan dan karakter polipeptida dari ketiga faktor transkripsi tersebut. Oleh karena itu, penelitian in-silico ini bertujuan untuk mengetahui hubungan filogenetik, serta karakteristik struktural dan fungsional dari GbMYB1, GbMYB2, dan GbMYC1. Analisis filogenetik menunjukkan kedekatan hubungan kekerabatan gen GbMYB1, GbMYB2, dan GbMYC1 dengan gen yang homolog pada beberapa spesies lainnya dari famili Asteraceae. Analisis fungsional menggunakan NCBI-CDD dan ExPASy-PROSITE pada sekuens peptidik GbMYB1 dan GbMYB2 menunjukkan adanya domain R2R3-MYB dengan motif anthocyanin-promoting MYB dan motif bHLH-interacting region. Sedangkan, GbMYC1 memiliki domain fungsional basic helix-loop-helix (bHLH). Sementara itu, analisis struktural menggunakan PSIPRED menunjukkan bahwa ketiga faktor transkripsi tersebut didominasi oleh struktur alpha-helix dan random coil. Prediksi model struktur tersier tiga dimensi menggunakan PHYRE2 pada GbMYB1, GbMYB2, serta GbMYC1 menunjukkan kualitas yang baik dengan nilai favoured region lebih dari 90% dan nilai QMEAN lebih besar dari -4.0. Hasil docking antara GbMYB1 dan GbMYB2 dengan model DNA PAL-Box masing-masing memiliki nilai Etotal = -3445.5 Kkal/mol dan Etotal = -3512.1 Kkal/mol yang menunjukkan kestabilan kompleks docking. Berdasarkan analisis karakteristik struktural dan fungsional, ketiga faktor transkripsi tersebut diketahui terlibat dalam regulasi biosintesis senyawa flavonoid pada G.bicolor.
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Flavonoid is a plant secondary metabolite compound with various benefits. Gynura bicolor from the Asteraceae family can act as a potential source for flavonoids. GbMYB1, GbMYB2, and GbMYC1 transcription factors have important roles in the accumulation of anthocyanins in G. bicolor. However, there is insufficient information regarding the relationship study and polypeptide character of these transcription factors. Therefore, this in-silico study aims to identify the phylogenetic relationship, as well as structural and functional characteristics of GbMYB1, GbMYB2, and GbMYC1. Phylogenetic analysis showed a close relationship between GbMYB1, GbMYB2, and GbMYC1 genes with their homologs in another species of the Asteraceae family. Functional analysis using NCBI-CDD and ExPASy PROSITE on GbMYB1 and GbMYB2 peptide sequences showed the presence of an R2R3-MYB domain with anthocyanin-promoting MYB and bHLH-interacting region motifs, while GbMYC1 has a basic helix-loop-helix (bHLH) functional domain. Structural analysis using PSIPRED showed that these transcription factors consist of predominantly alpha-helix and random coil structures. Three-dimensional tertiary structure model prediction of GbMYB1, GbMYB2, dan GbMYC1 using PHYRE2 all showed good results with favored region values of more than 90% and QMEAN values greater than -4.0. The docking results between GbMYB1 and GbMYB2 with the PAL-Box DNA model each have a value of Etotal = -3445.5 Kcal/mol and Etotal = -3512.1 Kcal/mol which indicates the stability of the docking complex. Based on the structural and functional analysis, these transcription factors are known to have roles in the flavonoid biosynthesis regulation of G. bicolor.
| Item Type: | Thesis (Undergraduate) |
|---|---|
| Uncontrolled Keywords: | faktor transkripsi, flavonoid, Gynura bicolor, pemodelan protein, protein modelling, transcription factor |
| Subjects: | Q Science > QH Biology > QH301 Biology Q Science > QK Botany Q Science > QP Physiology > QP624 Molecular biology. |
| Divisions: | Faculty of Science and Data Analytics (SCIENTICS) > Biology > 46201-(S1) Undergraduate Thesis |
| Depositing User: | Aulia Febrianti Widodo |
| Date Deposited: | 19 Aug 2021 05:14 |
| Last Modified: | 26 Aug 2021 02:41 |
| URI: | http://repository.its.ac.id/id/eprint/87692 |
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