International Journal of Innovative Approaches in Science Research
Abbreviation: IJIASR | ISSN (Print): 2602-4810 | ISSN (Online): 2602-4535 | DOI: 10.29329/ijiasr

Original article    |    Open Access
International Journal of Innovative Approaches in Science Research 2022, Vol. 6(2) 64-78

Identification and Bioinformatic Analysis of CAMTA Genes in Olive (Olea europaea L.)

Aslıhan Özbilen

pp. 64 - 78   |  DOI: https://doi.org/10.29329/ijiasr.2022.454.4

Published online: June 30, 2022  |   Number of Views: 6  |  Number of Download: 37


Abstract

Calcium is a secondary messenger which involves in stress response, adaptation, development and signaling pathways in plants. In cells, calcium is captured by calmodulin and after a conformation change, calmodulin becomes able to target calmodulin binding transcription factors. The calmodulin-binding transcriptional activators (CAMTAs) are one of these calmodulin binding transcription factors and they have CG-1, TIG, ANK, CaMBD and IQ conserved domains. CAMTAs are studied well in lots of plant species, and they are found to be involved in stress responses like drought, cold, salt and hormone responses like ethylene, abscisic acid, auxin, and gibberellin. In this study, CAMTA genes and proteins are characterized in olive. Olive (Olea europaea L.) is a Mediterranean commercially important crop, and this is the first study on olive CAMTAs. 7 CAMTA genes are found in olive in total in this study. Then, the cis-actin regulatory elements in the promoter regions of these genes are analyzed. Stress and hormone response related elements in the promoter regions are found, suggesting possible stress and hormone response roles of CAMTAs in olive. Also, protein characteristics, conserved domains, and subcellular localizations are investigated. According to the results, all olive CAMTA proteins are mainly localized in the nucleus as consistent with their roles, and all of them have 2 to 6 conserved domains which are also found in other plant CAMTAs. Additionally, a phylogenetic tree with 109 CAMTA proteins from well-knows plant species is constructed, and this tree showed that olive CAMTA proteins are highly conserved in plant kingdom.

Keywords: Calmodulin, CAMTA, Transcription Factor, Olive


How to Cite this Article

APA 6th edition
Ozbilen, A. (2022). Identification and Bioinformatic Analysis of CAMTA Genes in Olive (Olea europaea L.) . International Journal of Innovative Approaches in Science Research, 6(2), 64-78. doi: 10.29329/ijiasr.2022.454.4

Harvard
Ozbilen, A. (2022). Identification and Bioinformatic Analysis of CAMTA Genes in Olive (Olea europaea L.) . International Journal of Innovative Approaches in Science Research, 6(2), pp. 64-78.

Chicago 16th edition
Ozbilen, Aslihan (2022). "Identification and Bioinformatic Analysis of CAMTA Genes in Olive (Olea europaea L.) ". International Journal of Innovative Approaches in Science Research 6 (2):64-78. doi:10.29329/ijiasr.2022.454.4.

References
  1. Ali, E., Raza, M. A., Cai, M., Hussain, N., Shahzad, A. N., Hussain, M., ... & Sun, P. (2020). Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). Plos one, 15(7), e0236454. [Google Scholar]
  2. Bouché, N., Scharlat, A., Snedden, W., Bouchez, D., & Fromm, H. (2002). A novel family of calmodulin-binding transcription activators in multicellular organisms. Journal of Biological Chemistry, 277(24), 21851-21861. [Google Scholar]
  3. Büyük, İ., İlhan, E., Şener, D., Özsoy, A. U., & Aras, S. (2019). Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress. Molecular biology reports, 46(3), 2721-2732. [Google Scholar]
  4. D’Angeli, S., Malhó, R., & Altamura, M. M. (2003). Low-temperature sensing in olive tree: calcium signalling and cold acclimation. Plant Science, 165(6), 1303-1313. [Google Scholar]
  5. Doherty, C. J., Van Buskirk, H. A., Myers, S. J., & Thomashow, M. F. (2009). Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. The Plant Cell, 21(3), 972-984. [Google Scholar]
  6. Du, L., Yang, T., Puthanveettil, S. V., & Poovaiah, B. W. (2011). Decoding of calcium signal through calmodulin: calmodulin-binding proteins in plants. In Coding and decoding of calcium signals in plants (pp. 177-233). Springer, Berlin, Heidelberg. [Google Scholar]
  7. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797. [Google Scholar]
  8. Fang, H., Wang, P., Ye, F., Li, J., Zhang, M., Wang, C., & Liao, W. (2022). Genome-Wide Identification and Characterization of the Calmodulin-Binding Transcription Activator (CAMTA) Gene Family in Plants and the Expression Pattern Analysis of CAMTA3/SR1 in Tomato under Abiotic Stress. International Journal of Molecular Sciences, 23(11), 6264. [Google Scholar]
  9. Finkler, A., Ashery-Padan, R., & Fromm, H. (2007). CAMTAs: calmodulin-binding transcription activators from plants to human. FEBS letters, 581(21), 3893-3898. [Google Scholar]
  10. Gain, H., Nandi, D., Kumari, D., Das, A., Dasgupta, S. B., & Banerjee, J. (2022). Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure. Functional & Integrative Genomics, 22(2), 193-214. [Google Scholar]
  11. Galon, Y., Finkler, A., & Fromm, H. (2010). Calcium-regulated transcription in plants. Molecular Plant, 3(4), 653-669. [Google Scholar]
  12. Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook, 571-607. [Google Scholar]
  13. Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., ... & Rokhsar, D. S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic acids research, 40(D1), D1178-D1186. [Google Scholar]
  14. Kakar, K. U., Nawaz, Z., Cui, Z., Cao, P., Jin, J., Shu, Q., & Ren, X. (2018). Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses. Scientific reports, 8(1), 1-14. [Google Scholar]
  15. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., ... & Drummond, A. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28(12), 1647-1649. [Google Scholar]
  16. Kim, M. C., Chung, W. S., Yun, D. J., & Cho, M. J. (2009). Calcium and calmodulin-mediated regulation of gene expression in plants. Molecular plant, 2(1), 13-21. [Google Scholar]
  17. Kim, Y., Park, S., Gilmour, S. J., & Thomashow, M. F. (2013). Roles of CAMTA transcription factors and salicylic acid in configuring the low‐temperature transcriptome and freezing tolerance of A rabidopsis. The Plant Journal, 75(3), 364-376. [Google Scholar]
  18. Larbi, A., Kchaou, H., Gaaliche, B., Gargouri, K., Boulal, H., & Morales, F. (2020). Supplementary potassium and calcium improves salt tolerance in olive plants. Scientia Horticulturae, 260, 108912. [Google Scholar]
  19. Leng, X., Han, J., Wang, X., Zhao, M., Sun, X., Wang, C., & Fang, J. (2015). Characterization of a Calmodulin‐binding Transcription Factor from Strawberry (Fragaria× ananassa). The plant genome, 8(2), plantgenome2014-08. [Google Scholar]
  20. Methenni, K., Abdallah, M. B., Nouairi, I., Smaoui, A., Zarrouk, M., & Youssef, N. B. (2018). Salicylic acid and calcium pretreatments alleviate the toxic effect of salinity in the Oueslati olive variety. Scientia Horticulturae, 233, 349-358. [Google Scholar]
  21. Nie, H., Zhao, C., Wu, G., Wu, Y., Chen, Y., & Tang, D. (2012). SR1, a calmodulin-binding transcription factor, modulates plant defense and ethylene-induced senescence by directly regulating NDR1 and EIN3. Plant physiology, 158(4), 1847-1859. [Google Scholar]
  22. Pandey, N., Ranjan, A., Pant, P., Tripathi, R. K., Ateek, F., Pandey, H. P., ... & Sawant, S. V. (2013). CAMTA 1 regulates drought responses in Arabidopsis thaliana. BMC genomics, 14(1), 1-23. [Google Scholar]
  23. Pant, P., Iqbal, Z., Pandey, B. K., & Sawant, S. V. (2018). Genome-wide comparative and evolutionary analysis of calmodulin-binding transcription activator (CAMTA) family in Gossypium species. Scientific reports, 8(1), 1-17. [Google Scholar]
  24. Popescu, S. C., Popescu, G. V., Bachan, S., Zhang, Z., Seay, M., Gerstein, M., ... & Dinesh-Kumar, S. P. (2007). Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proceedings of the National Academy of Sciences, 104(11), 4730-4735. [Google Scholar]
  25. Primo-Capella, A., Martínez-Cuenca, M. R., & Forner-Giner, M. Á. (2021). Gene Expression under Short-Term Low Temperatures: Preliminary Screening Method to Obtain Tolerant Citrus Rootstocks. Horticulturae, 7(11), 447. [Google Scholar]
  26. Reddy, A. S. N., Reddy, V. S., & Golovkin, M. (2000). A calmodulin binding protein from Arabidopsis is induced by ethylene and contains a DNA-binding motif. Biochemical and biophysical research communications, 279(3), 762-769. [Google Scholar]
  27. Reddy, A. S., Ali, G. S., Celesnik, H., & Day, I. S. (2011). Coping with stresses: roles of calcium-and calcium/calmodulin-regulated gene expression. The Plant Cell, 23(6), 2010-2032. [Google Scholar]
  28. Rugini, E., (1986). Olive (Olea europeae L.). In: Bajaj Y.P.S, Ed. Biotechnology in Agriculture and Forestry, Springer, Heidelberg, pp 253- 267. [Google Scholar]
  29. Shangguan, L., Wang, X., Leng, X., Liu, D., Ren, G., Tao, R., ... & Fang, J. (2014). Identification and bioinformatic analysis of signal responsive/calmodulin-binding transcription activators gene models in Vitis vinifera. Molecular biology reports, 41(5), 2937-2949. [Google Scholar]
  30. Shen, C., Yang, Y., Du, L., & Wang, H. (2015). Calmodulin-binding transcription activators and perspectives for applications in biotechnology. Applied microbiology and biotechnology, 99(24), 10379-10385. [Google Scholar]
  31. Snedden, W. A., & Fromm, H. (2001). Calmodulin as a versatile calcium signal transducer in plants. New phytologist, 151(1), 35-66. [Google Scholar]
  32. Wang, G., Zeng, H., Hu, X., Zhu, Y., Chen, Y., Shen, C., ... & Du, L. (2015). Identification and expression analyses of calmodulin-binding transcription activator genes in soybean. Plant and soil, 386(1), 205-221. [Google Scholar]
  33. Wei, M., Xu, X., & Li, C. (2017). Identification and expression of CAMTA genes in Populus trichocarpa under biotic and abiotic stress. Scientific reports, 7(1), 1-10. [Google Scholar]
  34. Yang, T., & Poovaiah, B. W. (2002). A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants. Journal of Biological Chemistry, 277(47), 45049-45058. [Google Scholar]
  35. Yang, T., Peng, H., Whitaker, B. D., & Conway, W. S. (2012). Characterization of a calcium/calmodulin-regulated SR/CAMTA gene family during tomato fruit development and ripening. BMC plant biology, 12(1), 1-13. [Google Scholar]
  36. Yang, T., & Poovaiah, B. W. (2000). An early ethylene up-regulated gene encoding a calmodulin-binding protein involved in plant senescence and death. Journal of Biological Chemistry, 275(49), 38467-38473. [Google Scholar]
  37. Yang, F., Dong, F. S., Hu, F. H., Liu, Y. W., Chai, J. F., Zhao, H., ... & Zhou, S. (2020). Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.). BMC genetics, 21(1), 1-10. [Google Scholar]
  38. Yu, C. S., Chen, Y. C., Lu, C. H., & Hwang, J. K. (2006). Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3), 643-651. [Google Scholar]
  39. Yuan, J., Shen, C., Chen, B., Shen, A., & Li, X. (2021). Genome-Wide Characterization and Expression Analysis of CAMTA Gene Family Under Salt Stress in Cucurbita moschata and Cucurbita maxima. Frontiers in genetics, 12. [Google Scholar]
  40. Zielinski, R. E. (1998). Calmodulin and calmodulin-binding proteins in plants. Annual review of plant biology, 49(1), 697-725. [Google Scholar]
  41. Zhang, J., Pan, X. T., Ge, T., Yi, S. L., Lv, Q., Zheng, Y. Q., et al. (2019). Genomewide identification of citrus CAMTA genes and their expression analysis under stress and hormone treatments. J. Hortic. Sci. Biotech. 94, 331–340. doi: 10.1080/ 14620316.2018.1504631 [Google Scholar] [Crossref]