In silico study of RKD4 gene function in Coffea arabica L. and various cultivated plants related to embryo formation initiation
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Aug 30, 2024
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Abstract
Arabica coffee supplies 60% of world coffee production because has a unique taste as superior quality beverage. Arabica coffee micropropagation can be conducted by somatic embryogenesis technique which produce clonal, fast dan uniform plant. The somatic embryogenesis (SE) process describes the integration of endogenous signals and gene reprogramming, which releases signals to initiate embryogenic processes. The use of endogenous auxin, either alone or in combination with other PGRs or stress, induces differential gene expression, which modifies the genetic program of somatic cells and regulates the transition to each stage during SE development. The RKD4 gene (RWP-RK DOMAIN-4) is a gene that plays a role in early initiation embryo formation and development. The characterization of RKD4 genes in C. arabica is still limited and under explored. The objective of this research is to explore the characteristics of RKD4 gene by comparing the difference and similarity of RKD4 gene in C. arabica and other cultivated plants. The method was initiate by identifying nucleotide sequences from the National Center for Biotechnology Information (NCBI) database. Furthermore, consists of analysis of nucletide alignment, alignment of amino acid sequences, protein analysis, protein motif functions discovery, analysis of phylogenetic tree, protein 2D and 3D-modelling and physiochemical properties. According to the analysis, there were 100 polymorphism points with a total number of mutations of 211 points. The phylogenetic tree show C. arabica L. has a very close relationship with grapes (Vitis vinivera) based on the RKD4 protein, gene structures and protein motifs. There are nine highly conserved motifs found in the protein alignment. C. arabica L. had more methyl jasmonate element responses than A. thaliana. The findings are useful to understand the intitiation of embryo formation mechanisms of C. arabica L and other cultivate plants during propagation through somatic embryogenesis in the long run.
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Arimarsetiowati, R., Semiarti, E., Daryono, B., Astuti, Y., & Prastowo, E. (2024). In silico study of RKD4 gene function in Coffea arabica L. and various cultivated plants related to embryo formation initiation. Pelita Perkebunan (a Coffee and Cocoa Research Journal), 40(2), 105-124. https://doi.org/10.22302/iccri.jur.pelitaperkebunan.v40i2.600
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References
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Zimmerman, J. L. (1993). Somatic embryogenesis: a model for early development in higher plants. Plant cell, 5, 1411–1423.
Debnath, S.C. (2018) In thidiazuron: from urea derivative to plant growth regulator (eds. Naseem, A. & Mohammad, F.). Springer. 139–158.
Elhiti, M.; C. Stasolla & A. Wang (2013). Molecular regulation of plant somatic embryogenesis. In Vitro Cellular & Developmental Biology. Plant, 49, 631–642.
Horstman, A.; M. Bemer & K. Boutilier (2017). A transcriptional view on somatic embryogenesis. Regeneration, 4, 201–216.
Hu, B.; J. Jin; A.Y. Guo; H. Zhang; J. Luo & G. Gao (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31, 1296-1297.
Koi, S.; T. Hisanaga; K. Sato; M. Shimamura; K.T. Yamato; K. Ishizaki; T. Kohchi & K. Nakajima (2016). An evolutionarily conserved plant RKD factor controls germ cell differentiation. Current Biology, 26, 1–7.
Kőszegi, D.; A.J. Johnston; T. Rutten; L. Altschmied; J. Kumlehn; S.E.J. Wüst; O. Kirioukhova; J. Gheyselinck; U. Grossniklaus & H. Bäumlein (2011). Members of the RKD transcription factor family induce an egg cell‐like gene expression program. Plant Journal, 67, 280–291.
Leljak-Levanic, D.; S. Mihaljevic & N. Bauer (2015). Somatic and zygotic embryos share common developmental features at the onset of plant embryogenesis. Acta Physiologiae Plantarum, 37, 1–14.
Loyola-Vargas, V. M. & N. Ochoa-Alejo (2016). Somatic embryogenesis. An overview, in somatic embryogenesis. Fundamental Aspects and Applications, eds V. M. Loyola-Vargas and N. Ochoa-Alejo. Cham: Springer, 1–10.
Mursyanti, E.; A. Purwantoro; A. Moeljopawiro & E. Semiarti (2015). Induction of somatic embryogenesis through overexpression of AtRKD4 genes in Phalaenopsis “Sogo Vivien”. Indonesian Journal of Biotechnology, 20, 42-53.
Rozas, J.; A. Ferrer-Mata; J.C. Sánchez-DelBarrio; S. Guirao-Rico; P. Librado; S.E. Ramos-Onsins & A. Sánchez-Gracia (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34, 3299-3302.
Rövekamp, M.; J.L. Bowman & U. Grossniklaus (2016). Marchantia MpRKD regulates the gametophyte–sporophyte transition by keeping egg cells quiescent in the absence of fertilization. Current Biology, 26, 1–8.
Salaün, C.; L. Lepiniec & B. Dubreucq (2021). Genetic and molecular control of somatic embryogenesis. Plants, 10, 1467.
Seo, H. S.; J.T. Song; J.J. Cheong; Y.H. Lee; Y.W. Lee; I. Hwang; J.S. Lee & Y.D. Choi (2001). Jasmonic acid carboxyl methyltransferase: A key enzyme for jasmonate-regulated plant responses. Proceedings of the National Academy of Sciences, 98, 4788–4793.
Setiari, N.; A. Purwantoro; S. Moejopawiro & E. Semiarti (2018). Micropropagation of Dendrobium phalaenopsis orchid through overexpression of embryo gene AtRKD4. AGRIVITA Journal of Agricultural Science, 40, 284-294.
Smertenko, A. & P.V. Bozhkov (2014). Somatic embryogenesis: life and death processes during apical-basal patterning. Journal of Experimental Botany, 65, 1343–1360.
Tedeschi, F.; P. Rizzo; T. Rutten ; L. Altschmied & H. Bäumlein (2017). RWP-RK domain-containing transcription factors control cell differentiation during female gametophyte development in Arabidopsis. New Phytologist, 213, 1909–1924.
Trontin, J. F.; K. Klimaszewska; A. Morel; C. Hargreaves & M.A. Lelu-Walter (2016). Molecular aspects of conifer zygotic and somatic embryo development: a review of genome-wide approaches and recent insights, in In Vitro Embryogenesis in Higher Plants, eds M. A. Germanà and M. Lambardi. New York, NY: Springer, 167–207.
van der Vossen, H.; B. Bertrand & A. Charrier (2015). Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review. Euphytica, 204, 243–256.
Waki, T.; T. Hiki; R. Watanabe; T. Hashimoto & K. Nakajima (2011). The Arabidopsis RWP‐RK protein RKD4 triggers gene expression and pattern formation in early embryogenesis. Current Biology, 21, 1277–1281.
Wendrich, J. R. & D. Weijers (2013). The Arabidopsis embryo as a miniature morphogenesis model. New Phytologist, 199, 14–25.
Zhang, Q.; Z. Liang ;X. Cui; C. Ji; Y. Li; P. Zhang; J. Liu; A. Riaz; P. Yao; M. Liu; Y. Wang; T. Lu; H. Yu; D. Yang; H. Zheng & X. Gu (2018). N6-Methyladenine DNA methylation in Japonica and Indica rice genomes and its association with gene expression, plant development, and stress responses. Molecular Plant, 11, 1492–1508.
Zimmerman, J. L. (1993). Somatic embryogenesis: a model for early development in higher plants. Plant cell, 5, 1411–1423.
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