In silico study of RKD4 gene function in Coffea arabica L. and various cultivated plants related to embryo formation initiation
Article Sidebar
PDF
![Creative Commons License](//i.creativecommons.org/l/by-sa/4.0/88x31.png)
Published
Aug 30, 2024
DIMENSION
ALTMETRIC
Main Article Content
Rina Arimarsetiowati
Indonesian Coffee and Cocoa Research Institute
Endang Semiarti
Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada
Budi Setiadi Daryono
Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada
Yohana Theresia Maria Astuti
Faculty of Agriculture, Institut Pertanian Stiper (Instiper), Yogyakarta
Erwin Prastowo
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.
Article Details
How to Cite
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
Issue
Section
Articles
![Creative Commons License](http://i.creativecommons.org/l/by-sa/4.0/88x31.png)
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
References
Chardin, C.; T. Girin; F. Roudier; C. Meyer & A. Krapp (2014). The plant RWP-RK transcription factors: Key regulators of nitrogen responses of gametophyte development. Journal of Experimental Botany, 65, 5577–5587.
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.
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.
Most read articles by the same author(s)
- Rina Arimarsetiowati, Fitria Ardiyani, Pengaruh penambahan auxin terhadap pertunasan dan perakaran kopi arabika perbanyakan Somatic Embryogenesis (The effects of shooting and rooting of arabica coffee propagation through Embryogenesis Somatic auxin uses). , Pelita Perkebunan (a Coffee and Cocoa Research Journal): Vol 28 No 2 (2012)
- Rina Arimarsetiowati, Embryo Germination Development of Coffea arabica L.at Various Media Composition, Subcultures Stages and Embryo Size , Pelita Perkebunan (a Coffee and Cocoa Research Journal): Vol 33 No 3 (2017)
- Erwin Prastowo, Novie Pranata Erdiansyah, Rina Arimarsetiowati, Leaf Mineral Composition of Coffee Infected by a Hemileia vastatrix Fungus in Bondowoso, East Java , Pelita Perkebunan (a Coffee and Cocoa Research Journal): Vol 35 No 1 (2019)
- Erwin Prastowo, Rina Arimarsetiowati, Characteristics of coffee as a response to different environmental conditions in Lampung: I. Morphological variations , Pelita Perkebunan (a Coffee and Cocoa Research Journal): Vol 35 No 2 (2019)
- Erwin Prastowo, Rina Arimarsetiowati, Morphological Variations of Robusta Coffee As a Response to Different Altitude in Lampung , Pelita Perkebunan (a Coffee and Cocoa Research Journal): Vol 35 No 2 (2019)
- Rina Arimarsetiowati, Budi Setiadi Daryono, Yohana Theresia Maria Astuti, Endang Semiarti, Establishment of an efficient primary callus induction for embryogenic potential of Coffea arabica , Pelita Perkebunan (a Coffee and Cocoa Research Journal): Vol 38 No 2 (2022)