Transcriptional Regulation of Circadian Rhythm System for Developmental Stages in Cucumis melo L.: A Bioinformatic Study

Year 2024, , 879 - 887, 01.06.2024

Tugba Gürkök Tan , Ebru Derelli Tüfekçi

https://doi.org/10.21597/jist.1309061

Abstract

Circadian rhythm is defined biochemical, physiological, metabolic and behavioral responses of all living organisms such as bacteria, mammals, fungi and plants within a 24-hour light and dark photoperiod. In plants, circadian rhythm regulates multiple physiological, metabolic and behavioral processes such as stomatal and leaf movements, stem elongation, enzyme activity and aging. Circadian clock genes are known to play a role in regulating the biosynthesis of phytohormones which are involved in many crucial processes such as seed germination, hypocotyl elongation and photosynthesis. Circadian rhythm regulates and optimizes physiological and molecular mechanisms in a diurnal cycle, anticipating seasonal changes and preparing the plant for different environmental conditions in plant. Circadian rhythm also plays a crucial role in the regulation of plant defense against biotic and abiotic stresses. Melon is a diploid species and one of the most important Cucurbitaceae family members. In this study, we aimed to investigate the relationship between different developmental processes and circadian rhythm in melon. The relationship between circadian rhythm and growth, development and resistance in melon a detailed understanding of the relationship will help to improve future agricultural production and ground for further research on tolerance to environmental stresses will be created.

Keywords

Circadian rhythm, Developmental stage, Melon, Bioinformatic

Transcriptional Regulation of Circadian Rhythm System for Developmental Stage in Cucumis melo L. : A Bioinformatic Study

Abstract

References

• Atamian, H. S., Creux, N. M., Brown, E. A., Garner, A. G., Blackman, B. K. & Harmer, S. L. (2016). Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits. Science, 353(6299), 587-590.
• Chervin, C., El-Kereamy, A., Roustan, J. P., Latché, A., Lamon, J. & Bouzayen, M. (2004). Ethylene seems required for the berry development and ripening in grape, a non-climacteric fruit. Plant Science, 167(6), 1301-1305.
• Conesa, A., Gotz, S., Garcia-Gomez, J. M., Terol, J., Talon, M. & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674-3676.
• Farré, E. M., & Weise, S. E. (2012). The interactions between the circadian clock and primary metabolism. Current Opinion in Plant Biology, 15(3), 293-300.
• Fujiwara, S., Wang, L., Han, L., Suh, S. S., Salomé, P. A., McClung, C. R. & Somers, D. E. (2008). Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudoresponse regulator proteins. Journal of Biological Chemistry, 283(34), 1-11.
• Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G., González, V. M., Hénaff, E., Câmara, F., Cozzuto, L., Lowy, E., Alioto, T., CapellaGutiérrez, S., Blanca, J., Cañizares, J., Ziarsolo, P., Gonzalez-Ibeas, D., Rodríguez-Moreno, L., Droege, M., Du, L., Alvarez-Tejado, M., LorenteGaldos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez, F., Picó, B., Gabaldón, T., Roma, G., Guigó, R., Casacuberta, J. M., Arús, P. & Puigdomènech, P. (2012). The genome of melon (Cucumis melo L.). Proceedings of the National Academy of Sciences, 109(29), 11872-11877.
• Greenham, K., Sartor, R. C., Zorich, S., Lou, P., Mockler, T. C. & McClung, C. R. (2020). Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns. eLife https://elifesciences.org/articles/58993.
• Grundy, J., Stoker, C. & Carré, I. A. (2015). Circadian regulation of abiotic stress tolerance in plants. Frontiers in Plant Science, 6(648), 1-15.
• Harmer, S. L. (2009). The circadian system in higher plants. Annual Review of Plant Biology, 60(1), 357-377.
• Inoue, K., Araki, T. & Endo, M. (2017). Integration of input signals into the gene network in the plant circadian clock. Plant Cell Physiology, 58, 977-982.
• Karapetyan, S. & Dong, X. (2018). Redox and the circadian clock in plant immunity: A balancing act. Free Radical Biology and Medicine, 119, 56-61.
• Kazan, K. & Rebecca, L. (2016). The Link between Flowering Time and Stress Tolerance. Journal of Experimental Botany, 67(1), 47-60.
• Liu, X. (2001). ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. The Plant Cell Online, 13(6), 1293-1304.
• Mimida, N., Kidou, S. I., Iwanami, H., Moriya, S., Abe, K., Voogd, C., Varkonyi Gasic, E. & Kotoda, N. (2011). Apple FLOWERING LOCUS T proteins interact with transcription factors implicated in cell growth and organ development. Tree physiology, 31(5), 555-566
• Mishra, P. & Panigrahi, K. C. (2015). GIGANTEA - an Emerging Story. Frontiers in Plant Science, 6, 1-15.
• Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7), 621-628.
• Nimmo, H. G., Laird, J., Bindbeute,l R. & Nusinow, D. A. (2020). The evening complex is central to the difference between the circadian clocks of Arabidopsis thaliana shoots and roots. Physiologia Plantarum, 169(3), 442-451.
• Osorio, S., Scossa, F. & Fernie, A. R. (2013). Molecular regulation of fruit ripening. Frontiers in Plant Science, 4, 198.
• Pelvan, A., Bor, M., Yolcu, S., Özdemir, F. & Türkan, I. (2021). Day and night fluctuations in GABA biosynthesis contribute to drought responses in Nicotiana tabacum L. Plant Signaling & Behavior, 16(5), 1-9.
• Perales, M. & Más, Paloma. (2007). A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. The Plant Cell, 19(7), 211-2123.
• Périn, C., Gomez-Jimenez, M., Hagen, L., Dogimont, C., Pech, J. C., Latche, A., Pitrat, M. & Lelievre, J. M. (2002). Molecular and genetic characterization of a nonclimacteric phenotype in melon reveals two loci conferring altered ethylene response in fruit. Plant Physiology, 129, 300-309.
• Seymour, G., Taylor, J. E. & Tucker, G. A. (1993). Introduction. Biochemistry of Fruit Ripening. Chapman & Hall, 1-51, London.
• Sharma, M. & Bhatt, D. (2014). The circadian clock and defence signalling in plants. Molecular Plant Pathology, 16(2), 210-218.
• Srivastava, D., Shamim, M., Kumar, M., Mishra, A., Maurya, R., Sharma, D., Pandey, P. & Singh, K. N. (2019). Role of circadian rhythm in plant system: An update from development to stress response. Environmental and Experimental Botany, 162(2019), 256-271.
• Takada, S. & Goto, K. 2003. Terminal flower 2, an Arabidopsis homolog of heterochromatin protein1, counteracts the activation of flowering locus t by constans in the vascular tissues of leaves to regulate flowering time. Plant Cell, 15, 2856-2865.
• Tian, Y., Bai, S. L. G., Dang, Z. H., Hao, J. F., Zhang, J. & Hasi, A. (2019). Genome-wide identification and characterization of long non-coding RNAs involved in fruit ripening and the climacteric in Cucumis melo. BMC Plant Biology, 19(369), 1-15.
• Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38(16), e164-e164.