ANALYSIS OF DNA SEQUENCE ENCODING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDH) ON COCOR BEBEK (KALANCHOE x LAETIVIRENS)


Putri Agustina(1*), Dewi Indriyani Roslim(2),


(1) Universitas Riau
(2) Universitas Riau
(*) Corresponding Author

Abstract


To understand the fundamental mechanisms on genes in plant cells can be performed by gene expression studies. The study needs reference genes that act as internal control to avoid expression data bias. Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) gene is one of reference genes that has been validated in plants. This study aims to analyze the DNA sequences encoding GAPDH in cocor bebek (Kalanchoe x laetivirens). Methods included total DNA extraction from fresh leaf, polymerase chain reaction (PCR), electrophoresis at 1% agarose and DNA sequence data analysis. The DNA sequence of K. x laetivirens GAPDH gene obtained were 1107 bp and predicted to consist of 5 exons and 5 introns. This sequence had about 68.96%-73.81% similarity to the DNA sequence of the GAPDH gene in several plant species. The amino acid sequence of K. x laetivirens GAPDH had 5 conserved regions and residues of cysteine (C) and histidine. The sequence obtained in this study was the first to be reported from the genus Kalanchoe. This sequence can be used for analysis of gene expression in K. x laetivirens and can be as reference for isolating the GAPDH gene for other plant species in the genus Kalanchoe.

Keywords


Cocor bebek; GAPDH; Gen referensi; Kalanchoe x laetivirens; Kontrol internal; PCR

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References


Altschul, S.F. Madden, T.L. Schaffer, A.A. Zhang, J. Zhang, Z. Miller, W. & Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acid Research. 25(17): 3389-3402.

Aman, S. Haq, U.I. Ahmad & Shakeel, S.N. (2017). Identification and Validation of Reference Genes of Gene Expression Data Normalization of Chenopodium album. Int. Journal Agricultural, Biomolecular. 19: 761-770.

Azrial. (2018). Isolasi Gen Housekeeping Gliseraldehid-3-Fosfat Dehidrogenase (GAPDH) pada durik-durik (Syzygiumi sp.) asal Danau Kajuik Kabupaten Pelalawan Provinsi Riau. Skripsi. Universitas Riau.

Bao, W. Qu, Y. Shan, X. & Wan, Y. (2016). Screening and Validation of Housekeeping Genes of the Root and Cotyledon of Cunninghamia Lanceolata Under Abiotic Stresses by Using Quantitative real-time PCR. Int. J. Mol. Sci 17.

Basa, B. Solti, A. Sarvari, E. & Tamas L. (2009). Housekeeping Gene Selection in Poplar Plants under Cd-Stress Comparative Study for real-time PCR Normalisation. Functional Plant Biology. 36: 1079-1087.

Chervoneva, I. Li, Y. Schulz, S. Croker, S. Wilson, C. Waldman, S.A &Hyslop T. (2010). Selection of Optimal Reference Genes for Normalization in Quantitative RT-PCR. BMC Biofarma. 11: 253.

Claverie, J.M & Noterdame, C. (2007). Bioinformatics for Dummies, 2nd Editions. Indianapolis, Indiana: Wiley Publishing, Inc.

Court, D. (2000). Succulent flora of southern Africa. Rotterdam: A.A Balkema Publishers.

Darmayani, S., Shofi, M., & Raharjeng, A. R. P. (2018, November). RAPD Analysis of the Genetic Diversity Among Accessions of Micropropagation Bananas from Indonesia. In Journal of Physics: Conference Series (Vol. 1114, No. 1, p. 012137). IOP Publishing. Gantasala, N.P. Papolu, P.K. Thakur, P. K. Kamaraju, D. Sreevathsa, R. & Rao U. (2013). Selection and Validation of Reference Genes of Gene Expression Quantative Gene Expression Studies by real-time PCR in (Solanum melongena L.). BMC Research Notes. 6: 312-322.

Hall, T.A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows. Nucleic Acids Symposium Series. 41: 95-98.

Koressaar, T. Lepamets, M. Kaplinski, L. Raime, K. Andreson, R. & Remm, M. (2018). Primer3._Masker: Integrating Masking of Template Sequence with Primer Design Software. Bioinformatics. 34(11): 1937-1938.

Kozera, B & Rapacz M. (2013). Reference Genes in real-time PCR. Journal of Applied Genetics. 54(4): 391-406.

Libault, M. Thibivilliers, S. Bilgin, D.D. Radwan, O. Benit, M. Clough, S.J & Stacey, G. (2008). Identification of Four Soybean Reference Genes for Gene Expression Normalization. The Plant Genome. 1(1ilad, R., Ahmady, S. E dan Singab, A. N., (2014). Genus Kalanchoe (Crassulaceae): A Review it’s Ethnomedicinal, Botanical, Chemical and Pharmacological Properties. European Journal of Medicinal Plants. 4(1): 86-104.

Kosova, A.A. Khodyreva, S.N & Lavrik OI. (2017). Role of Glyceraldehide-3-Phosphate Dehydrogenase (GAPDH) in DNA repair. Biochemistry. 82(6): 643-654.

Lim, C.S. Wardell, S.J.T. Kleffman, T. & Brown, C.M. (2018). The exon and intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic acid research. 46(9): 4575-4591.

Madden, T. (2013). The NCBI handbook, 2nd editions. Bethesda (MD): National Center for Biotechnology Information (US).

Meng, H. Yang Y. Gao, Z.H. & Wei, J.H. (2019) Selection and Validation of Reference Genes for Gene Expression Study by Qrt-PCR in Dalbergia odorifera. Scientific Reports.9(1): 3341.

Petersen, J. Teich, R. Becker, B & Cerff, R. (2003). Origin, Evolution, and Metabolik Role of Novel Glycolytic GAPDH Enzyme Recruited by Land Plant Plastids. Journal MolEvol. 57: 16-26.

Purwoko, D. Cartealy, I.C. Tajjudin, T. Dinarti, D & Sudarsono. (2018). Analisis Bioinformatika Berbasis Web pada Sekuen Genom Parsial Sagu (Metroxylon Sagu Rottb.). Jurnal bioteknologi dan biosains Indonesia. 5(1): 98-107.

Raouf, Abdel H.S. (2011). Anatomical Traits of Some Species Kalanchoe (Crasulaceae) and their Taxonomic Value. Oroginal Article Annal Of Agricultural Science. 5(1): 73-79.

Roslim, D.I & Herman. (2017). Application of rps16 Intron and trnl-trnf Intergenic Spacer Sequences to Identify Rengas clone Riau. Journal of biology and biology education. 9(2): 209-216.

Roslim, D.I. Asih, H & Herman. (2020a). Sekuen DNA Parsial dari Gen GAPDH pada Sirsak (Annona muricata L.). Jurnal Biologi. 13(2): 209-217.

Roslim, D.I & Herman, Altuhaish A.A. (2020b). cDNA Sequences of Housekeeping Genes Act, GAPDH, and Ubq from Pandan (Benstonea sp.) Originating from Riau, Indonesia. SABRAO journal of breeding and genetics. 52(3): 292-310.

Roslim, D. I., Hairima, H., Herman, H., & Lestari, W. (2020c). The DNA Sequence Encoding Glyceraldehyde 3-Phosphate Dehydrogenase (Gapc) Enzyme On Tuntun Angin Plant (Elaeocarpus Floribundus BI). BIOLINK (Jurnal Biologi Lingkungan Industri Kesehatan), 7(1), 16-22.

Sikand, K. Singh, J. Ebron, J.S & Shukla, G.C. (2012). Housekeeping Gene Selection Advisory: gliseraldehid-3-fosfat dehidrogenase (GAPDH) and β-actin are Target of mir-644a. Plos One. 7(10): 1-9.

Singh, S. Gupta, M. Pandher, S. Kaur, G. Rathore, P & Palli, S.R. (2018). Selection of Housekeeping Genes and Demonstration of RNAi in cotton leafhopper, Arasca biguttula biguttula (Ishida). Plos One 13(1):1-21.

Sirover, M.A. (2011). One the Functional Diversity of Glyceraldehide-3-Phosphate Dehydrogenase: Biochemical Mechanisms and Regulatory Control. Biochimica et Biophysica Acta. 18(10): 741-751.

Tamura, K. Stecher, G. Peterson, D. Filipski, A & Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis versi 6.0. Molecular Biology and Evolution. 30(12): 2725-2729.

Tang, X. Zhang, N. Si, H. & Urrea A.C. (2017). Selection and Validation of Reference Genes for RT-qPCR Analysis in Potato Under Abiotic Stress. Plant Method. 13(85): 1-8.

Thanonkeo, P. Monkeang, R. Saksirirat, W. Thanonkeo, S & Akiyama, K. (2010). Cloning and Molecular Characterization of Gliseraldehid-3-Fosfat Dehidrogenase Gene from Thermotolerant Mushroom, lentinus polychrous. African Journal of Biotechnology. 9 (22): 3242-3251.

Turkoglu, S.A & Kockar, F. (2012). Expression of GAPDH, β-2 actin and β-2 Microglobulin Genes under Chemically Induced Hypoxic Conditional in Hep3b and PC3 cells. Journal of applied Biological Science. 6(3): 1-6.

Untergasser, A. Cutcutache, I. Koressaar, T. Faircloth, B.C. Remm, M & Rozen, S.G. (2012). Primer3 New Capabilities and Interfaces. Nucleic Acid Reserah. 40(15): 1-12.

Zeng, L. Deng, R. Guo, Z. Yang, S & Deng, X. (2016). Genome-Wide Identification and Characterization of Glyceraldehide-3-Phosphate Dehydrogenase Genes Family in Wheat (Triticum aestivum). BMC Genomic. 17: 1-10.




DOI: https://doi.org/10.31289/biolink.v8i1.4964

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Fakultas Saintek, Program Studi Biologi, Universitas Medan Area

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