Transcriptome-wide identification and characterization of WD40 genes, as well as their tissue-specific expression profiles and responses to heat stress in Dimocarpus longan Lour.
DOI:
https://doi.org/10.15835/nbha49112191Keywords:
bioinformatics analysis; Dimocarpus longan Lour; gene expression; WD40 gene; thermal responseAbstract
The WD40 transcription factor (TF) family is widespread in plants and plays important roles in plant growth and development, transcriptional regulation, and tolerance to abiotic stresses. WD40 TFs have been identified and characterized in a diverse series of plant species. However, little information is available on WD40 genes from D. longan. In this study, a total of 45 DlWD40 genes were identified from D. longan RNA-Seq data, and further analysed by bioinformatics tools. Also, the expression patterns of DlWD40 genes in roots and leaves, as well as responses to heat stress, were evaluated using quantitative real-time PCR (qRT-PCR). We found that the 45 DlWD40 proteins, together with 80 WD40 proteins from Arabidopsis and Zea mays, could be categorized into six groups. Of these, the DlWD40-4 protein was highly homologous to Arabidopsis WDR5a, a protein participating in tolerance to abiotic stresses. Moreover, a total of 25 cis-acting elements, such as abiotic stress and flavonoid biosynthesis elements, were found in the promoters of DlWD40 genes. The DlWD40-33 gene is targeted by miR3627, which has been proposed to be involved in flavonoid biosynthesis. Using qRT-PCR, ten of the 45 DlWD40 genes were demonstrated to have diverse expression patterns between roots and leaves, and these ten DlWD40 genes could also respond to varying durations of a 38 °C heat stress in roots and leaves. The results reported here will provide a basis for the further functional verification of DlWD40 genes in D. longan.
References
An XH, Tian Y, Chen KQ, Wang XF, Hao YJ (2012). The apple WD40 protein MdTTG1 interacts with bHLH but not MYB proteins to regulate anthocyanin accumulation. Journal of Plant Physiology 169(7):710-717. https://doi.org/10.1016/j.jplph.2012.01.015
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020). TBtools - an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant S1674-2052(20):30187-30188. https://doi.org/10.1016/j.molp.2020.06.009
Chen JJ, Mei S, Hu YR (2020). 脱落酸激素诱导拟南芥幼苗中花青素的合成 [Abscisic acid induces anthocyanin synthesis in Arabidopsis seedlings]. Guihaia 40(08):1169-1180.
de Vetten N, Quattrocchio F, Mol J, Koes R (1997). The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants, and animals. Genes & Development 11(11):1422-1434. https://doi.org/10.1101/gad.11.11.1422
Feyissa BA, Arshad M, Gruber MY, Kohalmi SE, Hannoufa A (2019). The interplay between miR156/SPL13 and DFR/WD40-1 regulate drought tolerance in alfalfa. BMC Plant Biology 19(1):434. https://doi.org/10.1186/s12870-019-2059-5
Fonseca S, Rubio V (2019). Arabidopsis CRL4 complexes: surveying chromatin states and gene expression. Frontiers in Plant Science https://doi.org/10.3389/fpls.2019.01095
Higa LA, Zhang H (2007). Stealing the spotlight: CUL4-DDB1 ubiquitin ligase docks WD40-repeat proteins to destroy. Cell Division 2:5. https://doi.org/10.1186/1747-1028-2-5
Ho SC, Hwang LS, Shen YJ, Lin CC (2007). Suppressive effect of a proanthocyanidin-rich extract from longan (Dimocarpus longan Lour.) flowers on nitric oxide production in LPS-stimulated macrophage cells. Journal of Agricultural and Food Chemistry 55(26):10664-10670. https://doi.org/10.1021/jf0721186
Hu R, Xiao J, Gu T, Yu X, Zhang Y, Chang J, Yang G, He G (2018a). Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). BMC Genomics 19(1):803. https://doi.org/10.1186/s12864-018-5157-0
Hu Z, Zhao L, Hu Z, Wang K (2018b). Hierarchical structure, gelatinization, and digestion characteristics of starch from longan (Dimocarpus longan Lour.) seeds. Molecules 23(12):3262. https://doi.org/10.3390/molecules23123262
Huang F, Liu H, Zhang R, Dong L, Liu L, Ma Y, … Zhang M (2019). Physicochemical properties and prebiotic activities of polysaccharides from longan pulp based on different extraction techniques. Carbohydrate Polymers 206:344-351. https://doi.org/10.1016/j.carbpol.2018.11.012
Jaakola L, Pirttilä AM, Halonen M, Hohtola A (2001). Isolation of high-quality RNA from bilberry (Vaccinium myrtillus L.) fruit. Molecular Biotechnology 19(2):201-203. https://doi.org/10.1385/MB:19:2:201
Jue D, Sang X, Liu L, Shu B, Wang Y, Liu C, Xie J, Shi S (2018). Identification of WRKY gene family from Dimocarpus longan and its expression analysis during flower induction and abiotic stress responses. International Journal of Molecular Sciences 19(8):2169. https://doi.org/10.3390/ijms19082169
Kong D, Li M, Dong Z, Ji H, Li X (2015). Identification of TaWD40D, a wheat WD40 repeat-containing protein that is associated with plant tolerance to abiotic stresses. Plant Cell Reports 34(3):395-410. https://doi.org/10.1007/s00299-014-1717-1
Li Q, Zhao P, Li J, Zhang C, Wang L, Ren Z (2014). Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis. Molecular Genetics and Genomics 289(1):103-124. https://doi.org/10.1007/s00438-013-0789-x
Li WH, Yang J, Gu X (2005). Expression divergence between duplicate genes. Trends in Genetics 21(11):602-607. https://doi.org/10.1016/j.tig.2005.08.006
Lin Y, Lai Z (2013). Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.). PloS One 8(4):e60337. https://doi.org/10.1371/journal.pone.0060337
Liu WC, Zheng SQ, Yu ZD, Gao X, Shen R, Lu YT (2018). WD40-REPEAT 5a represses root meristem growth by suppressing auxin synthesis through changes of nitric oxide accumulation in Arabidopsis. The Plant Journal 93(5):883-893. https://doi.org/10.1111/tpj.13816
Liu XF, Feng C, Zhang MM, Yin XR, Xu CJ, Chen KS (2013). The MrWD40-1 gene of Chinese bayberry (Myrica rubra) interacts with MYB and bHLH to enhance anthocyanin accumulation. Plant Molecular Biology Reporter 31(6):1474-1484. Https://doi.org/10.1007/s11105-013-0621-0
Liu YC, Ma W, Niu JF, Li B, Zhou W, Liu S, … Wang ZZ (2020). Systematic analysis of SmWD40s, and responding of SmWD40-170 to drought stress by regulation of ABA- and H2O2-induced stomal movement in Salvia miltiorrhiza bunge. Plant Physiology and Biochemistry 153:131-140. https://doi.org/10.1016/j.plaphy.2020.05.017
Ma J, An K, Zhou JB, Wu NS, Wang Y, Ye ZQ, Wu YD (2019). WDSPdb: an updated resource for WD40 proteins. Bioinformatics 35(22):4824-4826. https://doi.org/10.1093/bioinformatics/btz460
Mongin AA, Dohare P, Jourd'heuil D (2012). Selective vulnerability of synaptic signaling and metabolism to nitrosative stress. Antioxidants & Redox Signalling 17(7):992-1012. https://doi.org/10.1089/ars.2012.4559
Nash P, Tang X, Orlicky S, Chen Q, Gertler FB, Mendenhall MD, … Tyers M (2001). Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414(6863):514-521. https://doi.org/10.1038/35107009
Ouyang Y, Huang X, Lu Z, Yao J (2012). Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice. BMC Genomics 13:100. https://doi.org/10.1186/1471-2164-13-100
Qin L, Sun L, Wei L, Yuan J, Kong F, Zhang Y, … Liu S (2020). Maize SRO1e represses anthocyanin synthesis through regulating the MBW complex in response to abiotic stress. The Plant Journal https://doi.org/10.1111/tpj.15083
Schaart JG, Dubos C, Romero De La Fuente I, van Houwelingen AM, de Vos RC, Jonker HH, … Bovy AG (2013). Identification and characterization of MYB-bHLH-WD40 regulatory complexes controlling proanthocyanidin biosynthesis in strawberry (Fragaria × ananassa) fruits. New Phytologist 197(2):454-467. https://doi.org/10.1111/nph.12017
Schmittgen TD, Livak KJ (2008). Analyzing real-time PCR data by the comparative C(T) method. Nature Protocols 3(6):1101-1108. https://doi.org/10.1038/nprot.2008.73
Sunitha S, Loyola R, Alcalde JA, Arce-Johnson P, Matus JT, Rock CD (2019). The role of UV-B light on small RNA activity during grapevine berry development. G3: Genes, Genomes, Genetics 9(3):769-787. https://doi.org/10.1534/g3.118.200805
Tao N, Zhu W, Gan M, Chen M, Li T, Tendu A… Yang Q (2019). Genome-wide identification and functional analysis of the WDR protein family in potato. 3 Biotech 9(11):432. https://doi.org/10.1007/s13205-019-1965-4
Tossi V, Amenta M, Lamattina L, Cassia R (2011). Nitric oxide enhances plant ultraviolet-B protection up-regulating gene expression of the phenylpropanoid biosynthetic pathway. Plant, Cell & Environment 34(6):909-921. https://doi.org/10.1111/j.1365-3040.2011.02289.x
van Nocker S, Ludwig P (2003). The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. BMC Genomics 4(1):50. https://doi.org/10.1186/1471-2164-4-50
Wang B, Tan HW, Fang W, Meinhardt LW, Mischke S, Matsumoto T, Zhang D (2015). Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm. Horticulture Research 2:14065. https://doi.org/10.1038/hortres.2014.65
Wang L, Tang W, Hu Y, Zhang Y, Sun J, Guo X, … Liu Y (2019). A MYB/bHLH complex regulates tissue-specific anthocyanin biosynthesis in the inner pericarp of red-centered kiwifruit Actinidia chinensis cv. Hongyang. The Plant Journal 99(2):359-378. https://doi.org/10.1111/tpj.14330
Wang M, Gao Y, Qu P, Qing S, Qiao F, Zhang Y, Mager J, Wang Y (2017). Sperm-borne miR-449b influences cleavage, epigenetic reprogramming and apoptosis of SCNT embryos in bovine. Scientific Reports 7(1):13403. https://doi.org/10.1038/s41598-017-13899-8
Wu H, Lv H, Li L, Liu J, Mu S, Li X, Gao J (2015). Genome-wide analysis of the AP2/ERF Transcription factors family and the expression patterns of DREB genes in moso bamboo (Phyllostachys edulis). PloS One 10(5):e0126657. https://doi.org/10.1371/journal.pone.0126657
Xia KW (2019). 拟南芥WD40家族蛋白TAWD在抵御高温胁迫中的功能研究 [Function study of the WD40-repeat protein TAWD in Arabidopsis thermotolerance]. Central China Normal University.
Xu W, Grain D, Bobet S, Le Gourrierec J, Thévenin J, Kelemen Z, Lepiniec L, Dubos C (2014). Complexity and robustness of the flavonoid transcriptional regulatory network revealed by comprehensive analyses of MYB-bHLH-WDR complexes and their targets in Arabidopsis seed. New phytologist 202(1):132-144. https://doi.org/10.1111/nph.12620
Xue Y, Wang W, Liu Y, Zhan R, Chen Y (2015). Two new flavonols glycosides from Dimocarpus longan leaves. Natural Product Research 29(2):163-168. https://doi.org/10.1080/14786419.2014.971318
Yan J, He L, Xu S, Wan Y, Wang H, Wang Y, Yu L, Zhu W (2020). Expression analysis, functional marker development and verification of AgFNSI in celery. Scientific Reports 10(1):531. https://doi.org/10.1038/s41598-019-57054-x
Yuan F, Leng B, Zhang H, Wang X, Han G, Wang B (2019). A WD40-repeat protein from the recretohalophyte Limonium bicolor enhances trichome formation and salt tolerance in Arabidopsis. Frontiers in Plant Science 10:1456. https://doi.org/10.3389/fpls.2019.01456
Zheng W, Xie, TT, Yu XF, Ning C, Zhang ZW (2020). Characterization of bZIP transcription factors from Dimocarpus longan Lour. and analysis of their tissue-specific expression patterns and response to heat stress. Journal of Genetics 99:69. https://doi.org/10.1007/s12041-020-01229-3
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Copyright (c) 2021 Wei ZHENG, Ziwei ZHANG, Xuefei YU, Tongtong XIE, Ning CHEN, Wenlan LI
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