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Comparative bioinformatic research of gene promoters of DREB2B transcription factors in Deschampsia antarctica and some other cereals

Bublyk O.M., Andreev I.O., Kunakh V.A.

 




SUMMARY. The organization of promoters of DREB2B TF orthologous genes involved in the response to abiotic stress was studied in extremophile plant D. antarctica E. Desv and 12 other grass species with different cold and drought resistance. The average evolutionary distances were 0.621 between the promoter sequences and 0.442 between coding sequences, including introns; the values of nucleotide diversity (π) for these regions were 0.410 and 0.274, respectively. Clustering of sequences was generally consistent with the accepted taxonomy of the Poaceae family. In total, 54 cis-elements involved in the response to abiotic and biotic stresses, light, hormones, such as abscisic acid, auxin, methyl jasmonate, ethylene, gibberellin and salicylic acid, and tissue-specific cis elements were identified. A large proportion of these cis elements were associated with abiotic stress response that is consistent with known functions of DREB2B TF. Except for a few isolated differences, the studied grass species of different subfamilies and D. antarctica had a similar set of cis elements in the DREB2B promoter, a finding that indicates the similarity in the control of this gene expression and its potential functions in these species.

Key words: abiotic and biotic stress, DREB2B transcription factors, cis regulatory elements, grasses

Tsitologiya i Genetika 2022, vol. 56, no. 5, pp. 3-15

  • Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, 03143 Ukraine

E-mail: o.m.bublyk imbg.org.ua

Bublyk O.M., Andreev I.O., Kunakh V.A. Comparative bioinformatic research of gene promoters of DREB2B transcription factors in Deschampsia antarctica and some other cereals, Tsitol Genet., 2022, vol. 56, no. 5, pp. 3-15.

In "Cytology and Genetics":
O. M. Bublyk, I. O. Andreev & V. A. Kunakh Comparative Analysis of Promoters of DREB2B Transcription Factor Genes in Deschampsia antarctica and Other Grasses, Cytol Genet., 2022, vol. 56, no. 5, pp. 399–409
DOI: 10.3103/S0095452722050048


References

Akbudak, M.A., Filiz, E., and Kontbay, K., DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum (Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses, 3 Biotech, 2018, vol. 8, no. 10, art. ID 426. https://doi.org/10.1007/s13205-018-1454-1

Alves, G.S.C., Torres, L.F., de Aquino, S.O., et al., Nucleotide diversity of the coding and promoter regions of DREB1D, a candidate gene for drought tolerance in Coffea species, Trop. Plant Biol., 2018, vol. 11, pp. 31–48. https://doi.org/10.1007/s12042-018-9199-x

Bertini, L., Cozzolino, F., Proietti, S., et al., What antarctic plants can tell us about climate changes: temperature as a driver for metabolic reprogramming, Biomolecules, 2021, vol. 11, no. 8, art. ID 1094. https://doi.org/10.3390/biom11081094

Binenbaum, J., Weinstain, R., and Shani, E., Gibberellin localization and transport in plants, Trends Plant Sci., 2018, vol. 23, no. 5, pp. 410–421. https://doi.org/10.1016/j.tplants.2018.02.005

Bublyk, O.M., Andreev, I.O., and Kunakh, V.A., In silico identification and analysis of stress-inducible DREB2 transcription factors genes in Deschampsia antarctica Desv., in Factors in Experimental Evolution of Organisms, 2016, vol. 19, pp. 202–207. (in Ukrainian)

Camacho, C., Coulouris, G., Avagyan, V., et al., BLAST+: architecture and applications, BMC Bioinf., 2009, vol. 10, art. ID 421. https://doi.org/10.1186/1471-2105-10-421

Dubois, M., Van den Broeck, L., and Inzé, D., The pivotal role of ethylene in plant growth, Trends Plant Sci., 2018, vol. 23, no. 4, pp. 311–323. https://doi.org/10.1016/j.tplants.2018.01.003

Edgar, R.C., MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinf., 2004, vol. 5, art. ID 113. https://doi.org/10.1186/1471-2105-5-113

Egawa, C., Kobayashi, F., Ishibashi, M., et al., Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat, Genes Genet. Syst., 2006, vol. 81, no. 2, pp. 77–91. https://doi.org/10.1266/ggs.81.77

Emenecker, R.J. and Strader, L.C., Auxin-abscisic acid interactions in plant growth and development, Biomolecules, 2020, vol. 10, no. 2, art. ID 281. https://doi.org/10.3390/biom10020281

Erpen, L., Devi, H.S., Grosser, J.W., et al., Potential use of the DREB/ERF, MYB, NAC and WRKY transcription factors to improve abiotic and biotic stress in transgenic plants, Plant Cell, Tiss. Organ Cult., 2018, vol. 132, pp. 1–25. https://doi.org/10.1007/s11240-017-1320-6

Feng, K., Hou, X.-L., Xing, G.-M., et al., Advances in AP2/ERF super-family transcription factors in plant, Crit. Rev. Biotechnol., 2020, vol. 40, no. 6, pp. 750–776. https://doi.org/10.1080/07388551.2020.1768509

Filiz, E. and Tombuloğlu, H., In silico analysis of DREB transcription factor genes and proteins in grasses, Appl. Biochem. Biotechnol., 2014, vol. 174, pp. 1272–1285. https://doi.org/10.1007/s12010-014-1093-x

Herath, V., Small family, big impact: In silico analysis of DREB2 transcription factor family in rice, Comput. Biol. Chem., 2016, vol. 65, pp. 128–139. https://doi.org/10.1016/j.compbiolchem.2016.10.012

Jung, W.J. and Seo, Y.W., Identification of novel C-repeat binding factor (CBF) genes in rye (Secale cereale L.) and expression studies, Gene, 2019, vol. 684, pp. 82–94. https://doi.org/10.1016/j.gene.2018.10.055

Kim, H.-J., Kim, Y.-K., Park, J.-Y., and Kim, J., Light signalling mediated by phytochrome plays an important role in cold-induced gene expression through the C-repeat/dehydration responsive element (C/DRE) in Arabidopsis thaliana, Plant J., 2002, vol. 29, no. 6, pp. 693–704. https://doi.org/10.1046/j.1365-313X.2002.01249.x

Kovalchuk, N., Jia, W., Eini, O., et al., Optimization of TaDREB3 gene expression in transgenic barley using cold-inducible promoters, Plant Biotechnol. J., 2013, vol. 11, no. 6, pp. 659–670. https://doi.org/10.1111/pbi.12056

Kumar, S., Stecher, G., Li, M., et al., MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096

Lee, J., Kang, Y., Shin, S.C., et al., Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia เntarctica Desv., PLoS One, 2014, vol. 9, no. 6, art. ID e101100. https://doi.org/10.1371/journal.pone.0092501

Lescot, M., Déhais, P., Thijs, G., et al., PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences, Nucl. Acids Res., 2002, vol. 30, no. 1, pp. 325–327. https://doi.org/10.1093/nar/30.1.325

Li, C., Yue, J., Wu, X., et al., An ABA-responsive DRE-binding protein gene from Setaria italica, SiARDP, the target gene of SiAREB, plays a critical role under drought stress, J. Exp. Bot., vol. 65, no. 18, pp. 5415–5427. https://doi.org/10.1093/jxb/eru302

Matsukura, S., Mizoi, J., Yoshida, T., et al., Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes, Mol. Genet. Genomics, 2010, vol. 283, pp. 185–196. https://doi.org/10.1007/s00438-009-0506-y

Mohamed, H.I., El-Shazly, H.H., and Badr, A., Role of salicylic acid in biotic and abiotic stress tolerance in plants, in Plant Phenolics in Sustainable Agriculture, Lone, R., Shuab, R., and Kamili, A., Eds., Singapore: Springer-Verlag, 2020, pp. 533–554. https://doi.org/10.1007/978-981-15-4890-1_23

Book

Nakashima, K., Yusuke, I., and Yamaguchi-Shinozaki, K., Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses, Plant Physiol., 2009, vol. 149, no. 1, pp. 88–95. https://doi.org/10.1104/pp.108.129791

Nei, M., Molecular Evolutionary Genetics, New York: Columbia Univ. Press, 1987. https://doi.org/10.7312/nei-92038

Book

Neji, M., Geuna, F., Gandour, M., et al., Patterns of morpho-phenological and genetic variation of Brachypodium distachyon (L.) P.Beauv. complex in Tunisia, Genet. Resour. Crop Evol., 2022, vol. 69, pp. 577–586 doi.org/https://doi.org/10.1007/s10722-021-01242-0

Novillo, F., Alonso, J.M., Ecker, J.R., and Salinas, J., CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis, Proc. Natl. Acad. Sci. U. S. A., 2004, vol. 101, no. 11, pp. 3985–3990. https://doi.org/10.1073/pnas.0303029101

Ozheredova, I.P., Parnikoza, I.Yu., Poronnik, O.O., et al., Mechanisms of antarctic vascular plant adaptation to abiotic environmental factors, Cytol. Genet., 2015, vol. 49, no. 2, pp. 139–145. https://doi.org/10.3103/S0095452715020085

Pardo, J. and VanBuren, R., Evolutionary innovations driving abiotic stress tolerance in C4 grasses and cereals, Plant Cell, 2021, vol. 33, no. 11, pp. 3391–3401.https://doi.org/10.1093/plcell/koab205

Parnikoza, I., Kozeretska, I., and Kunakh, V., Vascular plants of the Maritime Antarctic: origin and adaptation, Am. J. Plant Sci., 2011, vol. 2, no. 3, pp. 381–395. https://doi.org/10.4236/ajps.2011.23044

Per, T.S., Khan, M.I.R., Anjum, N.A., et al., Jasmonates in plants under abiotic stresses: Crosstalk with other phytohormones matters, Environ. Exp. Bot., 2018, vol. 145, pp. 104–120. https://doi.org/10.1016/j.envexpbot.2017.11.004

Qin, F., Kakimoto, M., Sakuma, Y., et al., Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L., Plant J., 2007, vol. 50, no. 1, pp. 54–69. https://doi.org/10.1111/j.1365-313X.2007.03034.x

Roelofs, D., Morgan, J., and Sturzenbaum, S., The significance of genome-wide transcriptional regulation in the evolution of stress tolerance, Evol. Ecol., 2010, vol. 24, pp. 527–539. https://doi.org/10.1007/s10682-009-9345-x

Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., et al., DnaSP 6: DNA sequence polymorphism analysis of large data sets, Mol. Biol. Evol., 2017, vol. 34, no. 12, pp. 3299–3302. https://doi.org/10.1093/molbev/msx248

Saitou, N. and Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, vol. 4, no. 4, pp. 406–425.

Schubert, M., Grønvold, L., Sandve, S.R., et al., Evolution of cold acclimation and its role in niche transition in the temperate grass subfamily Pooideae, Plant Physiol., 2019, vol. 180, no. 1, pp. 404–419. https://doi.org/10.1104/pp.18.01448

Singh, K. and Chandra, A., DREBs-potential transcription factors involve in combating abiotic stress tolerance in plants, Biologia, 2021, vol. 76, pp. 3043–3055. https://doi.org/10.1007/s11756-021-00840-8

Tamura, K., Nei, M., and Kumar, S., Prospects for inferring very large phylogenies by using the neighbor-joining method, Proc. Natl. Acad. Sci. U. S. A., 2004, vol. 101, no. 30, pp. 11030–11035. https://doi.org/10.1073/pnas.0404206101

Tavakol, E., Sardaro, M.L.S., Shariati, V., et al., Isolation, promoter analysis and expression profile of Dreb2 in response to drought stress in wheat ancestors, Gene, 2014, vol. 549, no. 1, pp. 24–32. https://doi.org/10.1016/j.gene.2014.07.020

VanWallendael, A., Soltani, A., Emery, N.C., et al., A molecular view of plant local adaptation: Incorporating stress-response networks, Annu. Rev. Plant Biol., 2019, vol. 70, pp. 559–583. https://doi.org/10.1146/annurev-arplant-050718-100114

Walther, D., Brunnemann, R., and Selbig, J., The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana, PLoS Genet., 2007, vol. 3, no. 2, art. ID e11. https://doi.org/10.1371/journal.pgen.0030011

Wang, J., Song, L., Gong, X., Xu, J., and Li, M., Functions of jasmonic acid in plant regulation and response to abiotic stress, Int. J. Mol. Sci., 2020, vol. 21, no. 4, art. ID 1446. https://doi.org/10.3390/ijms21041446

Xiaxia, Y., Wenjin, Zh., Yu, Zh., et al., The roles of methyl jasmonate to stress in plants, Funct. Plant Biol., 2018, vol. 46, no. 3, pp. 197–212. https://doi.org/10.1071/FP18106

Xue, G.P. and Loveridge, C.W., HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element, Plant J., 2004, vol. 37, no. 3, pp. 326–339. https://doi.org/10.1046/j.1365-313X.2003.01963.x

Yamaguchi-Shinozaki, K., and Shinozaki, K., Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters, Trends Plant Sci., 2005, vol. 10, no. 2, pp. 88–94. https://doi.org/10.1016/j.tplants.2004.12.012

Yue, C., Cao, H., Lin, H., et al., Expression patterns of alpha-amylase and beta-amylase genes provide insights into the molecular mechanisms underlying the responses of tea plants (Camellia sinensis) to stress and postharvest processing treatments, Planta, 2019, vol. 250, pp. 281–298. https://doi.org/10.1007/s00425-019-03171-w

Zhang, N., McHale, L.K., and Finer, J.J., Changes to the core and flanking sequences of G-box elements lead to increases and decreases in gene expression in both native and synthetic soybean promoters, Plant Biotechnol. J., 2019, vol. 17, no. 4, pp. 724–735. https://doi.org/10.1111/pbi.13010

Zhang, Y. and Li, X., Salicylic acid: biosynthesis, perception, and contributions to plant immunity, Curr. Opin. Plant Biol., 2019, vol. 50, pp. 29–36. https://doi.org/10.1016/j.pbi.2019.02.004

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