[1]崔梦杰,王晨,冷翔鹏,等.葡萄SBP-box转录因子家族的生物信息学分析及其应答激素调控葡萄果实成熟的作用[J].南京农业大学学报,2018,41(3):429-439.[doi:10.7685/jnau.201706045]
 CUI Mengjie,WANG Chen,LENG Xiangpeng,et al.Bioinformatic analysis of the SBP-box transcription factor and function of their regulation modes on berry ripening process by responding to hormones[J].Journal of Nanjing Agricultural University,2018,41(3):429-439.[doi:10.7685/jnau.201706045]
点击复制

葡萄SBP-box转录因子家族的生物信息学分析及其应答激素调控葡萄果实成熟的作用()
分享到:

《南京农业大学学报》[ISSN:1000-2030/CN:32-1148/S]

卷:
41卷
期数:
2018年3期
页码:
429-439
栏目:
出版日期:
2018-05-15

文章信息/Info

Title:
Bioinformatic analysis of the SBP-box transcription factor and function of their regulation modes on berry ripening process by responding to hormones
作者:
崔梦杰1 王晨1 冷翔鹏1 吴伟民2 汤崴1 张文颖1 朱旭东1 贾海锋1 沈文飚3 房经贵1
1. 南京农业大学园艺学院, 江苏 南京 210095;
2. 江苏省农业科学院, 江苏 南京 210014;
3. 南京农业大学生命科学学院, 江苏 南京 210095
Author(s):
CUI Mengjie1 WANG Chen1 LENG Xiangpeng1 WU Weimin2 TANG Wei1 ZHANG Wenying1 ZHU Xudong1 JIA Haifeng1 SHEN Wenbiao3 FANG Jinggui1
1. College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
2. Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
3. College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
关键词:
葡萄SBP-box转录因子生物信息学分析表达分析
Keywords:
grape(Vitis vinifera L.)SBP-boxtranscription factorbioinformatic analysisexpression analysis
分类号:
S663.1
DOI:
10.7685/jnau.201706045
摘要:
[目的]本文旨在分析已知葡萄(Vitis vinifera L.)SBP-box家族基因基本信息,研究其在葡萄果实发育成熟过程中的调控作用。[方法]利用葡萄转录因子PlantTF数据库(http://planttfdb.cbi.pku.edu.cn/index.php?sp=Vvi)查询并获得SBP-box基因,采用ClustalX 2、DNAMAN 6、Web Logo 3、MEGA 4.1和Gene Structure Display Server等软件对其基因与蛋白序列进行生物信息学分析。利用Plantcare软件分析葡萄转录因子SBP-box家族成员的启动子元件,预测其与果实发育及成熟过程相关的潜在作用。采用RT-qPCR技术研究VvSBP基因在果实发育成熟过程中的作用。[结果]从转录因子数据库中共得到19个葡萄SBP-box基因。SBP-box结构域分析显示,多达61个位点氨基酸具有较高的保守性。进化树分析结果显示,葡萄SBP-box基因共分为3个亚组。染色体定位分析显示,VvSBP基因在1号染色体上分布最多(4个),其次是染色体5、15、4、7、8、10、11、12、14、17、18和19,染色体2、3、6、9、13和16则没有分布。启动子作用元件分析表明,SBP-box家族所有成员的启动子均含有与果实发育和成熟相关的作用元件。结合RT-qPCR结果,发现约9个成员可能促进了葡萄果实的成熟过程,且大部分成员属于第1亚组和第3亚组;约7个成员可能促进了葡萄果实的生长发育,但抑制了果实的转色与成熟过程,且大部分成员属于第2亚组。[结论]葡萄SBP-box基因结构高度保守,多数成员参与调控果实发育与成熟过程。
Abstract:
[Objectives] The aim of this paper is to analyze the basic information of SBP-box genes of grape(Vitis vinifera L.), and study their regulation function on berry ripening process. [Methods] SBP-box famiby genes in transcription factor database PlantTF(http://planttfdb.cbi.pku.edu.cn/index.php?sp=Vvi) were queried and obtained, and the amino acid sequences were analyzed with ClustalX 2, DNAMAN 6, Web Logo 3, MEGA 4.1 and Gene Structure Display Server bioinformatics softwares. The potential function of SBP-box transcription factor members in grape development and maturation process was predicted by analyzing their promoter motif elements using the Plantcare software. And the regulation function on berry ripening process was studied by RT-qPCR. [Results] Totally 19 SBP-box genes were found in transcription factor database. The results of domain analysis indicated that 48 amino acids of grape SBP-box domain were highly conserved(except for VvSBP-like1 and VvSBP-like2). The results of phylogenetic tree revealed that grape SBP-box genes were divided into 3 subclasses. Chromosome mapping analysis showed that the largest number of grape SBP-box genes were found on chromosome 1(four genes), followed by chromosome 5, 15, 4, 7, 8, 10, 11, 12, 14, 17, 18 and 19, and no SBP-box genes on chromosome 2, 3, 6, 9, 13 and 16. All SBP-box members contained elements related to grape berry development and ripening. RT-qPCR results indicated that nine members, the first and second subclass, probably promote berry ripening process, and nearly seven members, the second subclass, promote the growth and development of grape berry but inhibit the berry ripening process. [Conclusions] VvSBP genes are highly and structurally conserved and most members participated in regulating berry development and ripening process.

参考文献/References:

[1] 王发明. 我国鲜食葡萄生产现与发展趋势[J]. 西北园艺,2003(8):7-8. Wang F M. Production status and development trend of fresh grape in China[J]. Northwest Horticulture,2003(8):7-8(in Chinese).
[2] Huijser P,Klein J,Lönnig W E,et al. Bracteomania,an inflorescence anomaly,is caused by the loss of function of the MADS-box gene squamosa in Antirrhinum majus[J]. EMBO Journal,1992,11:1239-1249.
[3] Klein J,Saedler H,Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA[J]. Molecular and General Genetics,1996,250:7-16.
[4] Birkenbihl R P,Jach G,Saedler H,et al. Functional dissection of the plant-specific SBP-domain:overlap of the DNA-binding and nuclear localization domains[J]. Journal of Molecular Biology,2005,352:585-596.
[5] Wang J W,Czech B,Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana[J]. Cell,2009,138(4):738-749.
[6] Wang Y,Hu Z L,Yang Y X,et al. Bioinformatics analysis of SBP-box gene family in rice[J]. China Journal of Bioinformatics,2011,9(1):82-71.
[7] Shikata M,Koyama T,Mitsuda N,et al. Arabidopsis SBP-box genes SPL10,SPL11 and SPL2 control morphological change in association with shoot maturation in the reproductive phase[J]. Plant & Cell Physiology,2009,50(12):2133-2145.
[8] Gandikota M,Bitkenbihl R P,Hohmann S,et al. The miRNA156/157 recognition element in the 3’UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings[J]. Plant Journal,2007,49:683-693.
[9] 晁无疾,陆家云. 脱落酸(ABA)对葡萄上色和果实品质的影响[J]. 中外葡萄与葡萄酒,2008(5):285-287. Chao W J,Lu J Y. Effects of abscisic acid(ABA)on grape color and fruit quality[J]. Sino-Overseas Grapevine and Wine,2008(5):285-287(in Chinese).
[10] 王延书. 葡萄果实着色前后ABA代谢合成关键酶的基因表达分析[D]. 泰安:山东农业大学,2011. Wang Y S. Transcriptional analysis of key enzymes for ABA metabolism and biosynthesis around the veraison of grape berry ripening[D]. Tai’an:Shandong Agricultural University,2011(in Chinese with English abstract).
[11] 周莉,王军. NAA和ABA处理对‘京优’葡萄花色苷生物合成相关基因表达的影响[J]. 中国农业大学学报,2011,16(4):30-37. Zhou L,Wang J. Effects of NAA and ABA treatments on the expression of anthocyanin biosynthetic genes in ‘Jingyou’ grape berry skin[J]. Journal of China Agricultural University,2011,16(4):30-37(in Chinese with English abstract).
[12] 张彦苹,王晨,于华平,等. 适于葡萄不同组织RNA提取方法的筛选[J]. 西北农业学报,2010,19(11):135-140. Zhang Y P,Wang C,Yu H P,et al. Screening of RNA extraction methods for various grapevine organs and tissues[J]. Agriculturae Boreali-Occidentalis Sinica,2010,19(11):135-140(in Chinese with English abstract).
[13] Matsui K,Tanaka H,Ohme-Takagi M. Suppression of the biosynthesis of proanthocyanidin in Arabidopsis by a chimeric PAP1 repressor[J]. Plant Biotechnology Journal,2004,2(6):487-493.
[14] 吴蓓,李梦瑶,王广龙,等. 芹菜肉桂酰辅酶A还原酶基因的克隆与表达分析[J]. 南京农业大学学报,2016,39(6):907-914. DOI:10.7685/jnau.201603028. Wu B,Li M Y,Wang G L,et al. Cloning and the expression profiles analysis of an AgCCR gene encoding cinnamoyl-CoA reductase from different cultivars of Apium graveolens[J]. Journal of Nanjing Agricultural University,2016,39(6):907-914(in Chinese with English abstract).
[15] Livak K J,Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method[J]. Methods,2001,25:402-408.
[16] 贾海锋,刘众杰,赵鹏程,等. 转录因子ABI4调控草莓果实成熟的分子机制[J]. 南京农业大学学报,2015,38(6):908-914. DOI:10.7685/j.issn.1000-2030.2015.06.006. Jia H F,Liu Z J,Zhao P C,et al. The molecular mechanism of transcription factors ABI4 in regulation of strawberry fruit ripening[J]. Journal of Nanjing Agricultural University,2015,38(6):908-914(in Chinese with English abstract).
[17] Zhu X,Leng X,Sun X,et al. Discovery of conservation and diversification of miR171 genes by phylogenetic analysis based on global genomes[J]. The Plant Genome,2015,8(2):1-11.
[18] Tamura K,Dudley J,Nei M,et al. MEGA4:molecular evolutionary genetics analysis(MEGA)software version 4.0[J]. Molecular Biology and Evolution,2007,24(8):1596-1599.
[19] 曹雪,王晨,房经贵,等. 葡萄SPL9和SPL10基因全长cDNA克隆、亚细胞定位和表达分析[J]. 园艺学报,2011,38(2):240-250. Cao X,Wang C,Fang J G,et al. Cloning,subcellular localization and expression analysis of SPL9 and SPL10 genes from grapevine[J]. Acta Horticulturae Sinica,2011,38(2):240-250(in Chinese with English abstract).
[20] Kandori A,Miyashita T,Ogata K,et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening[J]. Nature Genetics,2006,38(8):948-952.
[21] Chen W,Kong J,Lai T,et al. Tuning LeSPL-CNR expression by SlymiR157 affects tomato fruit ripening[J]. Scientific Reports,2015,5:7852.
[22] Yamasaki K,Kigawa T,Inoue M,et al. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis,SBP-family transcription factors[J]. Journal of Molecular Biology,2004,337(1):49-63.

相似文献/References:

[1]宗成文,章镇,房经贵,等.葡萄LEAFY基因启动子的克隆与序列分析[J].南京农业大学学报,2007,30(4):20.[doi:10.7685/j.issn.1000-2030.2007.04.005]
 ZONG Cheng-wen,ZHANG Zhen,FANG Jing-gui,et al.Cloning and sequence analysis of LEAFY gene promoter from grape(Vitis vinifera×V.labrusca)[J].Journal of Nanjing Agricultural University,2007,30(3):20.[doi:10.7685/j.issn.1000-2030.2007.04.005]
[2]黄非,盛炳成.宿晓红葡萄与葡萄属有关种亲缘关系初探[J].南京农业大学学报,1993,16(04):49.[doi:10.7685/j.issn.1000-2030.1993.04.009]
 Huang Fei Sheng Bingcheng.STUDY ON THE RELATIONSHIP BETWEEN SUXIAOHONG GRAPE AND SOME SPECIES OF VITIS[J].Journal of Nanjing Agricultural University,1993,16(3):49.[doi:10.7685/j.issn.1000-2030.1993.04.009]
[3]周培根,戚晓玉,P.A.Braell,等.葡萄中β-damascenone前体的初步纯化[J].南京农业大学学报,1989,12(03):79.[doi:10.7685/j.issn.1000-2030.1989.03.017]
[4]韩浩章,姜卫兵,费宪进,等.葡萄和油桃自然休眠解除过程中H2O2含量和抗氧化酶活性的变化[J].南京农业大学学报,2007,30(1):50.[doi:10.7685/j.issn.1000-2030.2007.01.010]
 HAN Hao-zhang,JIANG Wei-bing,FEI Xianjin,et al.Changes in H_2O_2 content and activities of antioxidant enzymes of grape and nectarine during natural dormancy-release[J].Journal of Nanjing Agricultural University,2007,30(3):50.[doi:10.7685/j.issn.1000-2030.2007.01.010]
[5]郭磊,上官凌飞,房经贵*,等.葡萄EST鄄SSR 标记的开发及其应用[J].南京农业大学学报,2011,34(4):23.[doi:10.7685/j.issn.1000-2030.2011.04.005]
 GUO Lei,SHANGGUAN Ling-fei,FANG Jing-gui *,et al.Development of SSR markers from grape ESTs and its application[J].Journal of Nanjing Agricultural University,2011,34(3):23.[doi:10.7685/j.issn.1000-2030.2011.04.005]
[6]孙兴民,余智莹,张萌,等.葡萄未成熟胚诱导体细胞胚发生和植株再生与遗传鉴定[J].南京农业大学学报,2012,35(3):13.[doi:10.7685/j.issn.1000-2030.2012.03.003]
 SUN Xing-min,YU Zhi-ying,ZHANG Meng,et al.Somatic embryogenesis from immature zygotic embryos and genetic fidelity identificating of regenerated plants of grapevine[J].Journal of Nanjing Agricultural University,2012,35(3):13.[doi:10.7685/j.issn.1000-2030.2012.03.003]
[7]王晨,张演义,房经贵,等.葡萄microRNA156b和microRNA172c及其靶基因在冬芽二次成花过程中的表达特性研究[J].南京农业大学学报,2012,35(4):59.[doi:10.7685/j.issn.1000-2030.2012.04.011]
 WANG Chen,ZHANG Yan-yi,FANG Jing-gui,et al.Spatiotemporal expression of microRNA156b and microRNA172c and their target genes during flower development of winter buds growing on cut-back treated shoots of grapevine[J].Journal of Nanjing Agricultural University,2012,35(3):59.[doi:10.7685/j.issn.1000-2030.2012.04.011]
[8]王西成,王晨,房经贵,等.葡萄VvGA2ox1基因克隆、亚细胞定位及时空表达分析[J].南京农业大学学报,2013,36(1):29.[doi:10.7685/j.issn.1000-2030.2013.01.006]
 WANG Xicheng,WANG Chen,FANG Jinggui,et al.Cloning,subcellular localization and spatiotemporal expression of VvGA2ox1 gene from grapevine[J].Journal of Nanjing Agricultural University,2013,36(3):29.[doi:10.7685/j.issn.1000-2030.2013.01.006]
[9]谢荔,成学慧,冯新新,等.氨基酸肥料对‘夏黑’葡萄叶片光合特性与果实品质的影响[J].南京农业大学学报,2013,36(2):31.[doi:10.7685/j.issn.1000-2030.2013.02.006]
 XIE Li,CHENG Xuehui,FENG Xinxin,et al.Effects of an amino acid fertilizer on the leaf photosynthesis and fruit quality of ‘Summer Black’grape[J].Journal of Nanjing Agricultural University,2013,36(3):31.[doi:10.7685/j.issn.1000-2030.2013.02.006]
[10]任国慧,上官凌飞,房经贵,等.葡萄DELLA家族成员VvRGA和VvRGL1的预测、验证及生物信息学分析[J].南京农业大学学报,2013,36(3):15.[doi:10.7685/j.issn.1000-2030.2013.03.003]
 REN Guohui,SHANGGUAN Lingfei,FANG Jinggui,et al.The prediction,validation and bioinformatics analysis of the grape DELLA family members about VvRGA and VvRGL1[J].Journal of Nanjing Agricultural University,2013,36(3):15.[doi:10.7685/j.issn.1000-2030.2013.03.003]

备注/Memo

备注/Memo:
收稿日期:2017-06-29。
基金项目:中国博士后第七批特别资助项目(2014T70533);江苏省农业科技自主创新资金项目[CX(16)1013];国家博士后基金面上项目(2013M531373)
作者简介:崔梦杰,硕士研究生。
通信作者:王晨,副教授,研究方向为葡萄遗传育种与基因组学,E-mail:wangchen@njau.edu.cn。
更新日期/Last Update: 1900-01-01