* Corresponding Author
Mining GATA Transcription Factor Encoding Genes in The Cocoa Tree (Theobroma cacao L.) Suggests Their Potential Roles in Embryo Development and Biotic Stress Response
https://doi.org/10.22146/jtbb.88015 Ngoc Thi Bich Chu(1*), Thi Man Le(2), Ha Duc Chu(3), Huyen Thi Thanh Tran(4), Lan Thi Mai Tran(5), Hong Viet La(6), Quyen Thi Xuan Vu(7), Huynh Huy Phung(8), Phi Bang Cao(9)
(1) Faculty of Natural Sciences, Hung Vuong University, Phu Tho Province 35000, Vietnam
(2) Faculty of Natural Sciences, Hung Vuong University, Phu Tho Province 35000, Vietnam
(3) Faculty of Agricultural Technology, University of Engineering and Technology, Vietnam National University Hanoi, Xuan Thuy Road, Cau Giay District, Hanoi City 122300, Vietnam
(4) Faculty of Biology, Hanoi National University of Education, Xuan Thuy Road, Cau Giay District, Hanoi City 122300, Vietnam
(5) Faculty of Natural Sciences, Hung Vuong University, Phu Tho Province 35000, Vietnam
(6) Institute of Research and Application, Hanoi Pedagogical University 2, Phuc Yen City, Vinh Phuc Province 280000, Vietnam
(7) Faculty of Natural Sciences, Hung Vuong University, Phu Tho Province 35000, Vietnam
(8) Faculty of Natural Sciences, Hung Vuong University, Phu Tho Province 35000, Vietnam; Thanh Thuy Junior High School, Phu Tho Province 35000, Vietnam
(9) Faculty of Natural Sciences, Hung Vuong University, Phu Tho Province 35000, Vietnam
(*) Corresponding Author
Abstract
GATA transcription factors (TFs) are widely recognized as significant regulators, characterized by a DNA-binding domain that consists of a type IV zinc finger motif. This TF family has been widely investigated in numerous higher plant species. The purpose of the present work was to comprehensively analyze the GATA TF in cocoa plant (Theobroma cacao L.) by using various bioinformatics tools. As a result, a total of 24 members of the GATA TFs have been identified and annotated in the assembly of the cocoa plant. According to phylogenetic analysis, these TcGATA proteins were classified into four distinct groups, including groups I (10 members), II (seven members), III (five members), and IV (two members). Next, our investigation indicated that the TcGATA proteins in different groups exhibited a high variation in their physic-chemical features due to their different protein lengths, gene structures, and conserved motif distributions, whereas the TcGATA proteins in the same clade might share the common conserved motifs. Additionally, the gene duplication of the TcGATA genes in the cocoa plant was also investigated. Of our interest, the relative expression levels of the TcGATA genes were investigated according to available transcriptome databases. The results exhibited differential expression patterns of all TcGATA genes in various developmental stages of zygotic and somatic embryogenesis, indicating that these TcGATA genes divergently function during various developmental stages of the zygotic and somatic embryos. Moreover, TcGATA genes were differently expressed under Phytophthora megakarya treatment across different points of treatment and cocoa varieties. To sum up, our findings could provide a basis for a further deep understanding of the GATAs in the cocoa plant.
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Adeniyi, D., 2019. Diversity of cacao pathogens and impact on yield and global production. In Theobroma Cacao-Deploying Science for Sustainability of Global Cocoa Economy (pp. 1-20). doi: 10.5772/intechopen.81993
Bailey, T.L. et al., 2006. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res, 34(suppl 2), pp.W369-W373.
Barrett, T. et al., 2013. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res, 41(Database issue), pp.D991-D995. doi: 10.1093/nar/gks1193
Behringer, C. & Schwechheimer, C., 2015. B-GATA transcription factors – insights into their structure, regulation, and role in plant development. Frontiers in Plant Science, 6, 90. doi: 10.3389/fpls.2015.00090
Briesemeister, S. et al., 2009. SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. J Proteome Res, 8(11), pp.5363-5366. doi: 10.1021/pr900665y
Cao, P.B., 2022. In silico structural, evolutionary, and expression analysis of small heat shock protein (shsp) encoding genes in cocoa (Theobroma cacao L.). Journal of Animal and Plant Sciences, 32(5), pp.1394-1402. doi: 10.36899/JAPS.2022.5.0546
Chen, H. et al., 2017. Genome-wide identification, evolution, and expression analysis of GATA transcription factors in apple (Malus x domestica Borkh.). Gene, 627, pp.460-472. doi: 10.1016/j.gene.2017.06.049
Chiang, Y.H. et al., 2012. Functional Characterization of the GATA Transcription Factors GNC and CGA1 Reveals Their Key Role in Chloroplast Development, Growth, and Division in Arabidopsis. Plant Physiol, 160(1), pp.332-348. doi: 10.1104/pp.112.198705
Diaz-Valderrama, J.R. et al., 2020. The History of Cacao and Its Diseases in the Americas. Phytopathology, 110(10), pp.1604-1619. doi: 10.1094/PHYTO-05-20-0178-RVW
dos Santos, T.B. et al., 2022. Physiological responses to drought, salinity, and heat stress in plants: A review. Stresses, 2(1), pp.113-135. doi: 10.3390/stresses2010009
Du, X. et al., 2022. Genome-wide analysis of wheat GATA transcription factor genes reveals their molecular evolutionary characteristics and involvement in salt and drought tolerance. Int J Mol Sci, 24(1), 27. doi: 10.3390/ijms24010027
Fan, K. et al., 2014. Molecular evolution and expansion analysis of the NAC transcription factor in Zea mays. PLoS One, 9(11), e111837. doi: 10.1371/journal.pone.0111837
Feng, X. et al., 2022. Genome-wide identification and characterization of GATA family genes in wheat. BMC Plant Biol, 22(1), 372. doi: 10.1186/s12870-022-03733-3
Figueira, A. & Scotton, D. C., 2020. 13.1 Theobroma cacao Cacao. In Biotechnology of Fruit and Nut Crops (2 ed.). CABI, pp.282-313.
Gasteiger, E. et al., 2003. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res, 31(13), pp.3784-3788. doi: 10.1093/nar/gkg563
Gasteiger, E. et al., 2005. Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook. Springer, pp. 571-607.
Gertz, E.M. et al., 2006. Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST. BMC Biology, 4(1), 41. doi: 10.1186/1741-7007-4-41
Goodin, M.M., 2018. Chapter six - Protein localization and interaction studies in plants: Toward defining complete proteomes by visualization. Adv Virus Res, 100, pp.117-144. doi: 10.1016/bs.aivir.2017.10.004.
Goodstein, D.M. et al., 2012. Phytozome: A comparative platform for green plant genomics. Nucleic Acids Res, 40(Database issue), pp.D1178-D1186. doi: 10.1093/nar/gkr944
Guiltinan, M.J. et al., 2008. Genomics of Theobroma cacao, “the Food of the Gods”. In Genomics of Tropical Crop Plants. New York, USA: Springer New York, pp.145-170
Guo, M. et al., 2015. Genome-wide analysis of the CaHsp20 gene family in pepper: comprehensive sequence and expression profile analysis under heat stress. Front Plant Sci, 6, 806. doi: 10.3389/fpls.2015.00806
Gupta, P. et al., 2017. Abiotic stresses cause differential regulation of alternative splice forms of GATA transcription factor in rice. Front Plant Sci, 8, 1944. doi: 10.3389/fpls.2017.01944
Hu, B. et al., 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), pp.1296-1297. doi:10.1093/bioinformatics/btu817
Shi, M. et al., 2022. Genome-wide survey of the GATA gene family in camptothecin-producing plant Ophiorrhiza pumila. BMC Genomics, 23, 256. doi: 10.1186/s12864-022-08484-x
Jaimez, R.E. et al., 2022. Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects. PeerJ, 10, e12676. doi:10.7717/peerj.12676
Jin, J. et al., 2017. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 45(D1), pp.D1040-D1045. doi: 10.1093/nar/gkw982
Katoh, K. & Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 30(4), pp.772-780. doi: 10.1093/molbev/mst010
Kim, M. et al., 2021. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One, 16(5), e0252181. doi: 10.1371/journal.pone.0252181
Kim, M. et al., 2021. Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. Scientific Reports, 11(1), pp.1-15. doi: 10.1038/s41598-021-95940-5
Lai, D. et al., 2022. Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica). BMC Genomics, 23(1), 549. doi: 10.1186/s12864-022-08786-0
Le, T.M. et al. 2023. Comprehensive characterization and expression profiling of the GATA transcription factor in sugar beet (Beta vulgaris L.) suggests their potential roles in taproot development and biotic stress response. Jordan Journal of Biological Sciences, 16(4), pp.611-619. doi: 10.54319/jjbs/160406
Li, X. et al., 2023. Genome-wide identification and expression analysis of GATA gene family under different nitrogen levels in Arachis hypogaea L. Agronomy, 13(1), 215. doi: 10.3390/agronomy13010215
Liu, P.P. et al., 2005. The BME3 (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. Plant J, 44(6), pp.960-971. doi: 10.1111/j.1365-313X.2005.02588.x
Liu, X. et al., 2020. The wheat LLM-domain-containing transcription factor TaGATA1 positively modulates host immune response to Rhizoctonia cerealis. J Exp Bot, 71(1), pp.344-355. doi: 10.1093/jxb/erz409
Manzoor, M.A. et al., 2021. Comprehensive comparative analysis of the GATA transcription factors in four Rosaceae species and phytohormonal response in Chinese pear (Pyrus bretschneideri) fruit. Int J Mol Sci, 22(22), 12492. doi: 10.3390/ijms222212492
Maximova, S.N. et al., 2014. Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree. BMC Plant Biol, 14, 185. doi: 10.1186/1471-2229-14-185
Merika, M., & Orkin, S.H., 1993. DNA-binding specificity of GATA family transcription factors. Mol Cell Biol, 13(7), pp.3999-4010. doi: 10.1128/mcb.13.7.3999-4010.1993
Mistry, J. et al., 2021. Pfam: The protein families database in 2021. Nucleic Acids Res, 49(D1), pp.D412-D419. doi: 10.1093/nar/gkaa913
Motamayor, J.C. et al., 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol, 14(6), r53. doi: 10.1186/gb-2013-14-6-r53
Motamayor, J.C. et al., 2002. Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity (Edinb), 89(5), pp.380-386. doi: 10.1038/sj.hdy.6800156
Nawy, T. et al., 2010. The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Dev Cell, 19(1), pp.103-113. doi: 10.1016/j.devcel.2010.06.004
Niu, L. et al., 2020. The GATA gene family in chickpea: Structure analysis and transcriptional responses to abscisic acid and dehydration treatments revealed potential genes involved in drought adaptation. J Plant Growth Regul, 39(4), pp.1647-1660. doi: 10.1007/s00344-020-10201-5
Peng, W. et al., 2021. Genome-wide characterization, evolution, and expression profile analysis of GATA transcription factors in Brachypodium distachyon. Int J Mol Sci, 22(4), 2026. doi: 10.3390/ijms22042026
Pinheiro, T.T. et al., 2011. Establishing references for gene expression analyses by RT-qPCR in Theobroma cacao tissues. Genet Mol Res, 10(4), pp.3291-3305. doi: 10.4238/2011.November.17.4
Pokou, D.N. et al., 2019. Resistant and susceptible cacao genotypes exhibit defense gene polymorphism and unique early responses to Phytophthora megakarya inoculation. Plant Mol Biol, 99(4-5), pp.499-516. doi: 10.1007/s11103-019-00832-y
Pucciarelli, D.L., 2013. Cocoa and heart health: a historical review of the science. Nutrients, 5(10), pp.3854-3870. doi: 10.3390/nu5103854
Reyes, J.C. et al., 2004. The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol, 134(4), pp.1718-1732. doi: 10.1104/pp.103.037788
Rozas, J. et al., 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol, 34(12), pp.3299-3302. doi: 10.1093/molbev/msx248
Schwechheimer, C. et al., 2022. Plant GATA factors: Their biology, phylogeny, and phylogenomics. Annu Rev Plant Biol, 73, pp.123-148. doi: 10.1146/annurev-arplant-072221-092913
Shabbir, R. et al., 2022. Combined abiotic stresses: Challenges and potential for crop improvement. Agronomy, 12(11), 2795. doi: 10.3390/agronomy12112795
Tamura, K. et al., 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), pp.3022-3027. doi: 10.1093/molbev/msab120
Tan, T.Y.C et al., 2021. The health effects of chocolate and cocoa: A systematic review. Nutrients, 13(9), 2909. doi: 10.3390/nu13092909
Teakle, G.R. et al., 2002. Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics. Plant Mol Biol, 50(1), pp.43-57. doi: 10.1023/a:1016062325584
Wang, Q. et al., 2021. Genome-wide survey and characterization of ACD6-like genes in leguminous plants. Biologia, 76(10), pp.3137-3147. doi: 10.1007/s11756-021-00829-3
Wickramasuriya, A.M., & Dunwell, J.M., 2018. Cacao biotechnology: current status and future prospects. Plant Biotechnol J, 16(1), pp.4-17. doi:10.1111/pbi.12848
Yao, S. et al., 2021. NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. Nucleic Acids Res, 49(W1), pp.W469-W475. doi: 10.1093/nar/gkab398
Yu, C. et al., 2021. Genome-wide identification and function characterization of GATA transcription factors during development and in response to abiotic stresses and hormone treatments in pepper. J Appl Genet, 62(2), pp.265-280. doi: 10.1007/s13353-021-00618-3
Yu, R. et al., 2021. Genome-wide identification of the GATA gene family in potato (Solanum tuberosum L.) and expression analysis. J Plant Biotech Biochem, 31(1), pp.37-48. doi: 10.1007/s13562-021-00652-6
Zhang, C. et al., 2015. Genome-wide survey of the soybean GATA transcription factor gene family and expression analysis under low nitrogen stress. PLoS One, 10(4), e0125174. doi: 10.1371/journal.pone.0125174
Zhang, H. et al., 2021. OsGATA16, a GATA transcription factor, confers cold tolerance by repressing OsWRKY45–1 at the seedling stage in rice. Rice, 14(1), 42. doi: 10.1186/s12284-021-00485-w
Zhang, K. et al., 2021. Genome- wide identification, phylogenetic and expression pattern analysis of GATA family genes in cucumber (Cucumis sativus L.). Plants (Basel), 10(8). doi: 10.3390/plants10081626
Zhang, Z. et al., 2018. Characterization of the GATA gene family in Vitis vinifera: genome-wide analysis, expression profiles, and involvement in light and phytohormone response. Genome, 61(10), pp.713-723. doi: 10.1139/gen-2018-0042
Zhang, Z. et al., 2019. Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus. Gene, 680, pp.72-83. doi: 10.1016/j.gene.2018.09.039
Zhao, T. et al., 2021. Overexpression of SlGATA17 promotes drought tolerance in transgenic tomato plants by enhancing activation of the phenylpropanoid biosynthetic pathway. Front Plant Sci, 12, 634888. doi: 10.3389/fpls.2021.634888
Zhu, W. et al., 2020. Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus. BMC Plant Biology, 20(1), 543. doi: 10.1186/s12870-020-02752-2
DOI: https://doi.org/10.22146/jtbb.88015
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