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大白菜脱水素基因的鉴定和特征分析
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Abstract:
植物脱水素在非生物逆境响应过程中具有重要功能。但在我国重要蔬菜作物大白菜中缺乏研究。本文利用生物信息学的方法，鉴定出12个大白菜脱水素基因，对它们的结构特征、遗传进化和顺式调控元件进行了预测。结果显示，大白菜的脱水素基因在基因组中非均衡分布，大部分基因含有两个外显子，所有的大白菜脱水素可划分为两个不同的类群，其中BrDhn4单独为一个类群。顺式元件预测表明，大白菜脱水素基因含有多个响应环境和激素信号的顺式元件，可能在非生物逆境以及植物激素响应中具有一定功能。
Plant dehydrins play important roles in the process of abiotic stress responses. However, the dehy-drin knowledge about the important vegetable—Chinese cabbage is scarce. In this paper, 12 dehydrin genes were identified in the Chinese cabbage genome through the bioinformatics method. Also, their structure, phylogeny and the cis-elements of them were analyzed. The results indicated that Chinese cabbage dehydrin genes are unevenly distributed in the genome, and most of them have 2 exons. They are divided into two phylogeny groups, and BrDhn4 is singly as one group. What’s more, Chinese cabbage dehdrin genes each have several different cis-elements responsive to different hormones and environmental stimuli, which suggests they may be involved in multiple abiotic stress and hormone responses.
| [1] | Close, T.J. (1997) Dehydrins: A Commonality in the Response of Plants to Dehydration and Low Temperature. Physio-logia Plantarum, 100, 291-296. https://doi.org/10.1111/j.1399-3054.1997.tb04785.x |
| [2] | 马杰, 刘翠芳, 李灵之, 向建华, 陈信波. 非生物胁迫下植物脱水素的研究进展[J]. 生物学杂志, 2012, 29(1): 71-74. |
| [3] | Koag, M.C., Wilkens, S., Fenton, R.D., Resnik, J., Vo, E. and Close, T.J. (2009) The K-Segment of Maize DHN1 Mediates Binding to Anionic Phospholipid Vesicles and Concomitant Structural Changes. Plant Physiology, 150, 1503-1514.
https://doi.org/10.1104/pp.109.136697 |
| [4] | Eriksson, S., Eremina, N., Barth, A., Danielsson, J. and Harryson, P. (2016) Membrane-Induced Folding of the Plant Stress Dehydrin Lti30. Plant Physiology, 171, 932-943. https://doi.org/10.1104/pp.15.01531 |
| [5] | Zhai, C., Lan, J., Wang, H., Li, L., Cheng, X. and Liu, G. (2011) Rice Dehydrin K-Segments Have in vitro Antibacterial Activity. Biochemistry, 76, 645-650. https://doi.org/10.1134/S0006297911060046 |
| [6] | Drira, M., Saibi, W., Amara, I., Masmoudi, K., Hanin, M. and Brini, F. (2015) Wheat Dehydrin K-Segments Ensure Bacterial Stress Tolerance, Antiaggregation and Antimicrobial Ef-fects. Applied Biochemistry and Biotechnology, 175, 3310-3321. https://doi.org/10.1007/s12010-015-1502-9 |
| [7] | Alseikh, M.K., Svensson, J.T. and Randall, S.K. (2005) Phos-phorylation Regulated Ion-Binding Is a Property Shared by the Acidic Subclass Dehydrins. Plant, Cell and Environment, 28, 1114-1122.
https://doi.org/10.1111/j.1365-3040.2005.01348.x |
| [8] | Maszkowska, J., D？bski, J., Kulik, A., Kistowski, M., Bucholc, M., Lichocka, M., Klimecka, M., Sztatelman, O., Szymańska, K.P., Dadlez, M. and Dobrowolska, G. (2019) Phosphoproteomic Analysis Reveals That Dehydrins ERD10 and ERD14 Are Phosphorylated by SNF1-Related Protein Kinase 2.10 in Response to Osmotic Stress. Plant, Cell & Environment, 42, 931-946. https://doi.org/10.1111/pce.13465 |
| [9] | Kovacs, D., Kalmar, E., Torok, Z. and Tompa, P. (2008) Chaperone Activi-ty of ERD10 and ERD14, Two Disordered Stress-Related Plant Proteins. Plant Physiology, 147, 381-390. https://doi.org/10.1104/pp.108.118208 |
| [10] | Murvai, N., Kalmar, L., Szabo, B., Schad, E., Micsonai, A., Kardos, J., Buday, L., Han, K.H., Tompa, P. and Tantos, A. (2021) Cellular Chaperone Function of Intrinsically Disordered Dehy-drin ERD14. International Journal of Molecular Sciences, 22, Article 6190. https://doi.org/10.3390/ijms22126190 |
| [11] | Zaman Khan, N., Lal, S., Ali, W., Aasim, M., Mumtaz, S., Kamil, A. and Shad Bibi, N. (2020) Distribution and Classification of Dehydrins in Selected Plant Species Using Bioinformatics Approach. Iranian Journal of Biotechnology, 18, e2680. |
| [12] | Upadhyaya, G., Das, A., Basu, C., Agarwal, T., Basak, C., Chakraborty, C., Halder, T., Basu, G. and Ray, S. (2021) Multiple Copies of a Novel Amphipathic α-Helix Forming Segment in Physcomitrella patens Dehydrin Play a Key Role in Abiotic Stress Mitigation. Journal of Biological Chemis-try, 296, Article ID: 100596.
https://doi.org/10.1016/j.jbc.2021.100596 |
| [13] | Ohkubo, T., Kameyama, A., Kamiya, K., Kondo, M. and Hara, M. (2020) F-Segments of Arabidopsis Dehydrins Show Cryoprotective Activities for Lactate Dehydrogenase Depending on the Hydrophobic Residues. Phytochemistry, 173, Article ID: 112300. https://doi.org/10.1016/j.phytochem.2020.112300 |
| [14] | Wei, H., Yang, Y., Himmel, M.E., Tucker, M.P., Ding, S.Y., Yang, S. and Arora, R. (2019) Identification and Characterization of Five Cold Stress-Related Rhododendron De-hydrin Genes: Spotlight on a FSK-Type Dehydrin with Multiple F-Segments. Frontiers in Bioengineering and Biotech-nology, 7, Article 30.
https://doi.org/10.3389/fbioe.2019.00030 |
| [15] | 邢鑫, 刘洋, 李德全. 植物脱水素的结构和功能[J]. 植物生理学通讯, 2010, 46(3): 268-276. |
| [16] | 张琪, 周薇, 崔慧萍, 等. 不同类型脱水素在植物低温胁迫应答中的作用[J]. 核农学报, 2017, 31(4): 689-695. |
| [17] | 王西子, 信欣, 张方亦琢, 等. 植物脱水素的生物学功能与调控机制研究进展[J]. 植物生理学报, 2022, 58(9): 1617-1628. |
| [18] | Rorat, T. (2006) Plant Dehydrins—Tissue Location, Structure and Function. Cellular and Molecular Biology Letters, 11, 536-556. https://doi.org/10.2478/s11658-006-0044-0 |
| [19] | Yu, Z., Wang, X. and Zhang, L. (2018) Structural and Functional Dynamics of Dehydrins: A Plant Protector Protein under Abiotic Stress. International Journal of Molecular Sciences, 19, Article 3420.
https://doi.org/10.3390/ijms19113420 |
| [20] | Graether, S.P. and Boddington, K.F. (2014) Disorder and Function: A Review of the Dehydrin Protein Family. Frontiers in Plant Science, 5, Article 576. https://doi.org/10.3389/fpls.2014.00576 |
| [21] | Murray, M.R. and Graether, S.P. (2022) Physiological, Structural, and Functional Insights into the Cryoprotection of Membranes by the Dehydrins. Frontiers in Plant Science, 13, Article 886525. https://doi.org/10.3389/fpls.2022.886525 |
| [22] | Hanin, M., Brini, F., Ebel, C., Toda, Y., Takeda, S. and Masmoudi, K. (2011) Plant Dehydrins and Stress Tolerance: Versatile Proteins for Complex Mechanisms. Plant Signal-ing & Behavior, 6, 1503-1509.
https://doi.org/10.4161/psb.6.10.17088 |
| [23] | Smith, M.A. and Graether, S.P. (2022) The Disordered Dehydrin and Its Role in Plant Protection: A Biochemical Perspective. Biomolecules, 12, Article 294. https://doi.org/10.3390/biom12020294 |
| [24] | Sun, Z., Li, S., Chen, W., Zhang, J., Zhang, L., Sun, W. and Wang, Z. (2021) Plant Dehydrins: Expression, Regulatory Networks, and Protective Roles in Plants Challenged by Abiotic Stress. International Journal of Molecular Sciences, 22, Article 12619. https://doi.org/10.3390/ijms222312619 |
| [25] | Abdul Aziz, M., Sabeem, M., Mullath, S.K., Brini, F. and Masmoudi, K. (2021) Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses. Biomolecules, 11, Article 1662. https://doi.org/10.3390/biom11111662 |
| [26] | Liu, Y., Song, Q., Li, D., Yang, X. and Li, D. (2017) Multifunctional Roles of Plant Dehydrins in Response to Environmental Stresses. Frontiers in Plant Science, 8, Article 1018. https://doi.org/10.3389/fpls.2017.01018 |
| [27] | Abedini, R., Ghane Golmohammadi, F., PishkamRad, R., Pourabed, E., Jafarnezhad, A., Shobbar, Z.S. and Shahbazi, M. (2017) Plant Dehydrins: Shedding Light on Structure and Expres-sion Patterns of Dehydrin Gene Family in Barley. Journal of Plant Research, 130, 747-763. https://doi.org/10.1007/s10265-017-0941-5 |
| [28] | Kosová, K., Vítámvás, P. and Prá？il, I.T. (2014) Wheat and Barley Dehydrins under Cold, Drought, and Salinity—What Can LEA-II Proteins Tell Us about Plant Stress Response? Fron-tiers in Plant Science, 5, Article 343.
https://doi.org/10.3389/fpls.2014.00343 |
| [29] | Zaman, N., Lal, S., Ali, W., Aasim, M., Mumtaz, S., Kamil, A. and Bibi, N.S. (2020) Distribution and Classification of Dehydrins in Selected Plant Species Using Bioinformatics Approach. Iranian Journal of Biotechnology, 18, 56-66.
https://doi.org/10.30498/IJB.2020.2680 |
| [30] | Momma, M. (2019) Detection and Cryoprotective Activity of Dehy-drin Proteins from Rice Bran and Soybean Whey. Journal of Nutritional Science and Vitaminology, 65, S129-S133. https://doi.org/10.3177/jnsv.65.S129 |
| [31] | Decena, M.A., Gálvez-Rojas, S., Agostini, F., Sancho, R., Contre-ras-Moreira, B., Des Marais, D.L., Hernandez, P. and Catalán, P. (2021) Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses. Plants, 10, Article 2664. https://doi.org/10.3390/plants10122664 |
| [32] | Saruhan Güler, N., Terzi, R., Demiralay, M., Ozturk, K. and Kadioglu, A. (2022) Increased Dehydrin Level Decreases Leaf Rolling Grade by Altering the Reactive Oxygen Species Homeosta-sis and Abscisic Acid Content in Maize Subjected to Osmotic Stress. 3 Biotech, 12, Article No. 201. https://doi.org/10.1007/s13205-022-03275-3 |
| [33] | Yamasaki, Y., Koehler, G., Blacklock, B.J. and Randall, S.K. (2013) Dehydrin Expression in Soybean. Plant Physiology and Biochemistry, 70, 213-220. https://doi.org/10.1016/j.plaphy.2013.05.013 |
| [34] | Kartashov, A.V., Zlobin, I.E., Pashkovskiy, P.P., Pojidaeva, E.S, Ivanov Y.V, Mamaeva, A.S., Fesenko, I.A. and Kuznetsov, V.V. (2021) Quantitative Analysis of Differential Dehydrin Regulation in Pine and Spruce Seedlings under Water Deficit. Plant Physiology and Biochemistry, 162, 237-246. https://doi.org/10.1016/j.plaphy.2021.02.040 |
| [35] | Xu, Y.Y., Zeng, R.F., Zhou, H., Qiu, M.Q., Gan, Z.M., Yang, Y.L., Hu, S.F., Zhou, J.J., Hu, C.G. and Zhang, J.Z. (2022) Citrus FRIGIDA Cooperates with Its Interaction Partner Dehydrin to Regulate Drought Tolerance. The Plant Journal, 111, 164-182. https://doi.org/10.1111/tpj.15785 |
| [36] | Edrisi Maryan, K., Samizadeh Lahiji, H., Farrokhi, N. and Hasani Komeleh, H. (2019) Analysis of Brassica napus Dehydrins and Their Co-Expression Regulatory Networks in Relation to Cold Stress. Gene Expression Patterns, 31, 7-17. https://doi.org/10.1016/j.gep.2018.10.002 |
| [37] | Lu, Y., Sun, X., Yao, J., Chai, Y., Zhao, X., Zhang, L., Song, J., Pang, Y.Z., Wu, W. and Tang, K. (2003) Isolation and Expression of Cold-Regulated cDNA from Chinese Cabbage (Brassica pekinensis). DNA Sequence, 14, 219-222.
https://doi.org/10.1080/1042517031000095381 |
| [38] | Wang, X., Wang, H., Wang J., et al. (2011) The Genome of the Mesopolyploid Crop Species Brassica rapa. Nature Genetics, 43, 1035-1039. https://doi.org/10.1038/ng.919 |
| [39] | Cai, C.C., Wang, X.B., Liu, B., Wu, J., Liang, J.L., Cui, Y., Cheng, F. and Wang, X. (2017) Brassica rapa Genome 2.0: A Reference Upgrade through Sequence Re-Assembly and Gene Re-Annotation. Molecular Plant, 10, 649-651.
https://doi.org/10.1016/j.molp.2016.11.008 |
| [40] | Yang, Y., Liu, H., Wang, A. and Zhang, L. (2020) An ERF-Type Transcription Factor Is Involved in the Regulation of the Dehydrin Wzy1-2 Gene in Wheat. Plant Signaling & Behavior, 15, Article ID: 1778920.
https://doi.org/10.1080/15592324.2020.1778920 |
| [41] | Liu, H., Yang, Y., Liu, D., Wang, X. and Zhang, L. (2020) Transcription Factor TabHLH49 Positively Regulates Dehydrin WZY2 Gene Expression and Enhances Drought Stress Tolerance in Wheat. BMC Plant Biology, 20, Article 259. https://doi.org/10.1186/s12870-020-02474-5 |
| [42] | Nguyen, P.N., Tossounian, M.A., Kovacs, D.S., Thu, T.T., Stijlemans, B., Vertommen, D., Pauwels, J., Gevaert, K., Angenon, G., Messens, J. and Tompa, P. (2020) Dehydrin ERD14 Activates Glutathione Transferase Phi9 in Arabidopsis thaliana under Osmotic Stress. Biochimica et Biophysica Acta (BBA)—General Subjects, 1864, Article ID: 129506. https://doi.org/10.1016/j.bbagen.2019.129506 |
