萝卜TALE转录因子家族的鉴定与分析
作者:
基金项目:

国家自然科学基金(31772301);国家重点研发计划(2016YFD0100204-07);基本科研业务费(IVF-BRF2020001)


Identification and analysis of the TALE transcription factor family in radish
Author:
  • ZHAO Wei

    ZHAO Wei

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • LI Xixiang

    LI Xixiang

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • WANG Haiping

    WANG Haiping

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • JIA Huixia

    JIA Huixia

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • SONG Jiangping

    SONG Jiangping

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • YANG Wenlong

    YANG Wenlong

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • ZHANG Xiaohui

    ZHANG Xiaohui

    Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs of Peoples Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing 100081, China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • 摘要
  • | |
  • 访问统计
  • |
  • 参考文献 [28]
  • |
  • 相似文献 [20]
  • | | |
  • 文章评论
    摘要:

    TALE (three-amino acid loop extension) 转录因子在植物生长发育及细胞分化过程中起重要作用。在多种植物中均已鉴定出TALE转录因子的家族成员,但是萝卜TALE转录因子家族的研究鲜有报道。文中通过生物信息学手段在象牙白萝卜全基因组中鉴定出了分布于9条染色体上的33个TALE家族基因。研究结果显示,该家族中除与拟南芥KNATM同源的基因Rsa10037940外,其余基因均含有编码HOX保守结构域的序列。这些基因含有4–6个外显子。萝卜的33个TALE基因与拟南芥中的17个同源基因存在共线性关系。33个TALE基因启动子区的顺式元件中包含大量逆境响应元件。表达特性分析显示,该基因家族BELL亚家族内有4个基因在根内表达量较高,KNOX亚家族内有2个基因在薹和愈伤中表达量较高。该家族不同亚型成员之间的蛋白3D结构高度相似。编码蛋白均为弱酸、有亲水性。萝卜TALE基因家族在进化上较为保守,分化上与拟南芥存在一致性,与水稻差异较大。本研究为开展萝卜中TALE转录因子的生物学功能研究提供了重要参考。

    Abstract:

    Three-amino acid loop extension (TALE) transcription factors play important roles in plant growth and cell differentiation. There are plenty of studies on TALE transcription factors in several model plants, but not in radish (Raphanus sativas). A genome-wide bioinformatics analysis identified 33 TALE family genes in the Xiang-Ya-Bai (XYB) radish, These genes, are distributed on nine chromosomes and all contain 4-6 exons. The 33 TALE genes in radish showed a co-linearity relationship with the 17 homologous genes in Arabidopsis thaliana. Moreover, a large number of stress response cis-elements were found in the promoter regions of these genes. Expression analysis showed that four genes in the BELL subfamily were highly expressed in roots, and two genes in the KNOX subfamily were highly expressed in shoots of bolting plants and callus. All radish TALE genes contain sequences encoding the conserved HOX domain, except for the gene RSA10037940, which is homologous to Arabidopsis KNATM. The deduced 3D structures of the TALE proteins irrespective of subtypes are highly similar. All the encoded proteins were weakly acidic and hydrophilic. The radish TALE gene family is relatively evolutionarily conserved, which was consistent with results from Arabidopsis, but quite different from that of rice. This study provides important clues for studying the biological functions of TALE transcription factors in radish.

    参考文献
    [1] Billeter M, Qian YQ, Otting G, et al. Determination of the nuclear magnetic resonance solution structure of an antennapedia homeodomain-DNA complex. J Mol Biol, 1993, 234(4): 1084-1097.
    [2] Jin J, Feng T, De-Chang Y, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 2017: D1040-D1045.
    [3] Magnani E, Hake S. KNOX lost the OX: the Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain. Plant Cell, 2008, 20(4): 875-887.
    [4] Meng L, Fan Z, Zhang Q, et al. BEL1-LIKE HOMEODOMAIN 11 regulates chloroplast development and chlorophyll synthesis in tomato fruit. Plant J, 2018, 94(6): 1126-1140.
    [5] Zhao K, Zhang X, Cheng Z, et al. Comprehensive analysis of the three-amino-acid-loop-extension gene family and its tissue-differential expression in response to salt stress in poplar. Plant Physiol Biochem, 2019, 136: 1-12.
    [6] Zhang ZR, Ji XH, Zhang HY, et al. Bioinformatics analysis of TALE transcription factors in pepper. Mol Plant Breed, 2020, 18(5): 1401-1408 (in Chinese). 张中荣, 吉雪花, 张海英, 等. 辣椒TALE转录因子的生物信息学分析. 分子植物育种, 2020, 18(5): 1401-1408.
    [7] Qiu RG, Zhang TY, Yang SM, et al. Genome-wide identification and bioinformatics analysis of TALE transcription factor family in Lotus japonicus. J Plant Genet Resour, 2019, 20(2): 466-475 (in Chinese). 丘日光, 张天缘, 杨仕梅, 等. 百脉根TALE转录因子家族的鉴定与生物信息学分析. 植物遗传资源学报, 2019, 20(2): 466-475.
    [8] Ma Q, Wang N, Hao P, et al. Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis. BMC Plant Biol, 2019, 19(1): 432.
    [9] Zhang XH, Yue Z, Mei SY, et al. A de novo genome of a Chinese radish cultivar. Hortic Plant J, 2015, 1(3): 155-164.
    [10] Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 2020, 13(8): 1194-1202.
    [11] Sun Y, Wang J, Qiu Y, et al. Identification of 'Xinlimei' radish candidate genes associated with anthocyanin biosynthesis based on a transcriptome analysis. Gene, 2018, 657: 81-91.
    [12] Liu TT, Li XM, ZHang XH, et al. Genome-wide identification and analysis of SPL gene family in radish. J Plant Genet Resour, 2021, 22(4): 1145-1156 (in Chinese). 刘婷婷, 李晓曼, 张晓辉, 等. 萝卜全基因组中SPL基因家族成员的鉴定与分析. 植物遗传资源学报, 2021, 22(4): 1145-1156.
    [13] Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res, 2016, 44(w1): W242-W245.
    [14] Shani E, Yanai O, Ori N. The role of hormones in shoot apical meristem function. Curr Opin Plant Biol, 2006, 9(5): 484-489.
    [15] Chen H, Banerjee AK, Hannapel DJ. The tandem complex of BEL and KNOX partners is required for transcriptional repression of ga20ox1. Plant J, 2004, 38(2): 276-284.
    [16] Kumar R, Kushalappa K, Godt D, et al. The Arabidopsis BEL1-LIKE HOMEODOMAIN proteins SAW1 and SAW2 act redundantly to regulate KNOX expression spatially in leaf margins. Plant Cell, 2007, 19(9): 2719-2735.
    [17] Xu Y, Wang Y, Wang X, et al. Transcription factors BLH2 and BLH4 regulate demethylesterification of homogalacturonan in seed mucilage. Plant Physiol, 2020, 183(1): 96-111.
    [18] Souček P, Hanáček P, Mazura P, et al. Interaction among BREVIPEDICELLUS, BLH6 and auxin in roots of Arabidopsis thaliana. Russ J Plant Physiol, 2017, 64(3): 386-397.
    [19] Truernit E, Siemering KR, Hodge S, et al. A map of KNAT gene expression in the Arabidopsis root. Plant Mol Biol, 2006, 60(1): 1-20.
    [20] Postma-Haarsma AD, Verwoert Ⅱ, Stronk OP, et al. Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis. Plant Mol Biol, 1999, 39(2): 257-271.
    [21] Kim D, Cho YH, Ryu H, et al. BLH1 and KNAT3 modulate ABA responses during germination and early seedling development in Arabidopsis. Plant J, 2013, 75(5): 755-766.
    [22] Smith HMS, Campbell BC, Hake S. Competence to respond to floral inductive signals requires the homeobox genes pennywise and pound-foolish. Curr Biol, 2004, 14(9): 812-817.
    [23] Bhatt AM, Etchells JP, Canales C, et al. VAAMANA—a BEL1-like homeodomain protein, interacts with KNOX proteins BP and STM and regulates inflorescence stem growth in Arabidopsis. Gene, 2004, 328: 103-111.
    [24] Belles-Boix E, Hamant O, Witiak SM, et al. KNAT6: An Arabidopsis homeobox gene involved in meristem activity and organ separation. Plant Cell, 2006, 18(8): 1900-1907.
    [25] Li E, Bhargava A, Qiang W, et al. The Class Ⅱ KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus. New Phytol, 2012, 194(1): 102-115.
    [26] Wang YY, Zhao YJ, Yan M, et al. Genome-wide identification and expression analysis of TALE gene family in pomegranate (Punica granatum L. ). Agronomy, 2020, 10(6): 829.
    [27] Michelmore RW, Meyers BC. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res, 1998, 8(11): 1113-1130.
    [28] Deng L, Shen BQ, Wang LC, et al. Genome-wide bioinformatics analysis of AP2/EREBP transcription factor in 'Hongyang' kiwifruit. J Fruit Sci, 2017, 34(7): 790-805 (in Chinese). 邓浪, 沈兵琪, 王连春, 等. '红阳'猕猴桃全基因组AP2/EREBP转录因子生物信息学分析. 果树学报, 2017, 34(7): 790-805.
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

赵伟,李锡香,王海平,贾会霞,宋江萍,阳文龙,张晓辉. 萝卜TALE转录因子家族的鉴定与分析[J]. 生物工程学报, 2022, 38(1): 343-358

复制
分享
文章指标
  • 点击次数:487
  • 下载次数: 1586
  • HTML阅读次数: 1508
  • 引用次数: 0
历史
  • 收稿日期:2021-04-29
  • 在线发布日期: 2022-01-25
文章二维码
您是第6320112位访问者
生物工程学报 ® 2025 版权所有

通信地址:中国科学院微生物研究所    邮编:100101

电话:010-64807509   E-mail:cjb@im.ac.cn

技术支持:北京勤云科技发展有限公司