|本期目录/Table of Contents|

[1]朱芸晔,薛冰,王安全,等.番茄bZIP转录因子家族的生物信息学分析[J].应用与环境生物学报,2014,20(05):767-774.[doi:10.3724/SP.J.1145.2014.01033]
 ZHU Yunye,XUE Bing,WANG Anquan,et al.Comprehensive bioinformatic analysis of bZIP transcription factors in Solanum lycopersicum[J].Chinese Journal of Applied & Environmental Biology,2014,20(05):767-774.[doi:10.3724/SP.J.1145.2014.01033]
点击复制

番茄bZIP转录因子家族的生物信息学分析()
分享到:

《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
20卷
期数:
2014年05期
页码:
767-774
栏目:
研究论文
出版日期:
2014-10-25

文章信息/Info

Title:
Comprehensive bioinformatic analysis of bZIP transcription factors in Solanum lycopersicum
作者:
朱芸晔薛冰王安全王文杰周昂黄胜雄刘永胜
合肥工业大学生物与食品工程学院 合肥 230009
Author(s):
ZHU Yunye XUE Bing WANG Anquan WANG Wenjie ZHOU Ang HUANG Shengxiong LIU Yongsheng
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China 2University of Chinese Academy of Sciences, Beijing 100049, China
关键词:
番茄bZIP转录因子生物信息学分析
Keywords:
School of Biotechnology and Food Engineering Hefei University of Technology Hefei 230009 China
分类号:
S641.203.4
DOI:
10.3724/SP.J.1145.2014.01033
摘要:
bZIP转录因子广泛参与了植物生长发育以及抗逆应答的调控,属于重要的转录因子家族. 为了系统地阐明番茄bZIP转录因子家族成员特征和基因表达模式,利用生物信息学软件和方法,对番茄基因组中的bZIP转录因子进行了系统的分析研究. 结果表明:番茄基因组共编码70个bZIP转录因子基因,划分为14个亚族,即A、B、C、D、E、F、G、H、I、J、K、L、S和X. 番茄、拟南芥和水稻bZIP基因的系统进化树揭示了进化过程中Group 3和Group 4的成员数目大大增加,进化过程较激烈. 氨基酸保守域DOG1和MFMR分别特定存在于12个和6个bZIP成员蛋白序列中. 在番茄各器官组织中,干旱、盐、细菌和病毒侵染胁迫条件下,43个番茄bZIP基因不同程度地被诱导表达. 以基因表达值上调或下调1.5倍为阈值,部分bZIP基因的表达水平被显著地诱导上调或下调表达. 这些基因很可能参与了调控番茄的果实等组织的生长发育,以及逆境胁迫条件下的防御应答反应. 通过荧光实时定量PCR,其中7个代表性番茄bZIP基因,被进一步验证了在叶片和果实中的表达水平. 本研究鉴定得到的番茄bZIP转录因子基因,可用于今后番茄育种及改良的基因工程研究.
Abstract:
The bZIP transcription factors are important participants in regulating plant development and defense response against various biotic and abiotic stresses. The characterization and expression pattern of tomato bZIP transcription factors are not clear so far therefore needing systematic analysis. Using the bioinformatics softwares and methods, we performed comprehensive bioinformatic analysis for the bZIP transcription factors in Solanum lycopersicum. All together 70 tomato bZIP transcription factors were identified and classified into 14 groups, including A, B, C, D, E, F, G, H, I, J, K, L, S and X. The phylogenetic tree of bZIP genes among tomato, arabidopsis and rice demonstrated that the members in Group 3 and Group 4 largely expanded, implying sharp evolution process. In 12 and 6 tomato bZIP transcription factors, DOG1 and MFMR conserved motif existed, respectively. Furthermore, 43 tomato bZIP genes showed distinct expression patterns in various tomato organs and tissues, as well as under stresses of drought, salt, bacteria and virus invasion. Under the criteria of change ration (1.5), the expressions of several tomato bZIP genes were significantly up/down-regulated, implying these members might participate in regulating tomato development, and the defense response against various biotic and abiotic stresses. The expression of 7 representative tomato bZIP genes in different tissues was validated by real time quantitative RT-PCR. Our study could provide bZIP genes for further genetic engineering study of tomato breeding and improvement.

参考文献/References:

1 The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution [J]. Nature, 2012, 485: 635-641
2 Foster R, Izawa T, Chua NH. Plant bZIP proteins gather at ACGT elements [J]. FASEB J, 1994, 8 (2): 192-200
3 Silveira AB, Gauer L, Tomaz JP, Cardoso PR, Carmello-Guerreiro S, Vincentz M. The Arabidopsis AtbZIP9 protein fused to the VP16 transcriptional activation domain alters leaf and vascular development [J]. Plant Sci, 2007, 172 (6): 1148-1156
4 Chuang CF, Running MP, Williams RW, Meyerowitz EM. The PERIANTHIA gene encodes a bZIP protein involved in the determination of floral organ number in Arabidopsis thaliana [J]. Genes Dev, 1999, 13 (3): 334-344
5 Shen H, Cao K, Wang X. A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer [J]. Biochem Biophys Res Commun, 2007, 362 (2): 425-430
6 Kaminaka H, N?ke C, Epple P, Dittgen J, Schütze K, Chaban C, Holt BF 3rd, Merkle T, Sch?fer E, Harter K, Dangl JL. bZIP10-LSD1 antagonism modulates basal defense and cell death in Arabidopsis following infection [J]. EMBO J, 2006, 25 (18): 4400-4411
7 Liu JX, Srivastava R, Che P, Howell SH. Salt stress responses in Arabidopsis utilize a signal transduction pathway related to endoplasmic reticulum stress signaling [J]. Plant J, 2007, 51 (5): 897-909
8 Weltmeier F, Ehlert A, Mayer CS, Dietrich K, Wang X, Schütze K, Alonso R, Harter K, Vicente-Carbajosa J, Dr?ge-Laser W. Combinatorial control of Arabidopsis proline dehydrogenase transcription by specific heterodimerisation of bZIP transcription factors [J]. EMBO J, 2006, 25 (13): 3133-3143
9 Iwata Y, Koizumi N. An Arabidopsis transcription factor, AtbZIP60, regulates the endoplasmic reticulum stress response in a manner unique to plants [J]. Proc Natl Acad Sci USA, 2005, 102 (14): 5280-5285
10 Ulm R, Baumann A, Oravecz A, Máté Z, Adám E, Oakeley EJ, Sch?fer E, Nagy F. Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis [J]. Proc Natl Acad Sci USA, 2004, 101 (5): 1397-1402
11 Jakoby M, Weisshaar B, Dr?ge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F; bZIP Research Group. bZIP transcription factors in Arabidopsis [J]. Trends Plant Sci, 2002, 7 (3): 106-111
12 Corrêa LG, Ria?o-Pachón DM, Schrago CG, dos Santos RV, Mueller-Roeber B, Vincentz M. The role of bZIP transcription factors in green plant evolution adaptive features emerging from four founder genes [J]. PLoS ONE, 2008, 3 (8): e2944
13 Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ,Ghandehari D, Sherman BK, Yu G. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes [J]. Science, 2000, 290 (5499): 2105-2110
14 Wei K, Chen J, Wang Y, Chen Y, Chen S, Lin Y, Pan S, Zhong X, Xie D. Genome-wide analysis of bZIP-encoding genes in maize [J]. DNA Res, 2012, 19 (6): 463-476
15 Nijhawan A, Jain M, Tyagi AK, Khurana JP. Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice [J]. Plant Physiol, 2008, 146 (2): 333-350
16 Wang J, Zhou J, Zhang B, Vanitha J, Ramachandran S, Jiang SY. Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum [J]. J Integr Plant Biol, 2011, 53 (3): 212-231
17 Liao Y, Zou HF, Wei W, Hao YJ, Tian AG, Huang J, Liu YF, Zhang JS, Chen SY. Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis [J]. Planta, 2008, 228 (2): 225-240
18 Deppmann CD, Alvania RS, Taparowsky EJ. Cross-ecies annotation of basic leucine zipper factor interactions: insight into the evolution of closedinteraction networks [J]. Mol Biol Evol, 2006, 23 (8): 1480-1492
19 Sell S, Hehl R. Functional dissection of a small anaerobically indu-ced bZIP transcription factor from tomato [J]. Eur J Biochem, 2004, 271 (22): 4534-4544
20 Liu Y, Roof S, Ye Z, Barry C, van Tuinen A, Vrebalov J, Bowler C, Giovannoni J. Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato [J]. Proc Natl Acad Sci USA, 2004, 101 (26): 9897-9902
21 Stankovi? B, Vian A, Henry-Vian C, Davies E. Molecular clon-ing and characterization of a tomato cDNA encoding a systemically wound-inducible bZIP DNA-binding protein [J]. Planta, 2000, 212 (1): 60-66
22 Seong ES, Kwon SS, Ghimire BK, Yu CY, Cho DH, Lim JD, Kim KS, Heo K, Lim ES, Chung IM, Kim MJ, Lee YS. LebZIP2 induced by salt and drought stress and transient overexpression by Agrobacterium [J]. BMB Rep, 2008, 41 (10): 693-698
23 Orellana S, Ya?ez M, Espinoza A, Verdugo I, González E, Ruiz-Lara S, Casaretto JA. The transcription factor SlAREB1 confers drought, salt stress tolerance and regulates biotic and abiotic stress-related genes in tomato [J]. Plant Cell Environ, 2010, 33 (12): 2191-2208
24 黄胜雄, 刘永胜. 土豆WRKY转录因子家族的生物信息学分析[J]. 应用与环境生物学报, 2013, 19 (2): 205-214 [Huang SX, Liu YS. Genome-wide analysis of WRKY transcription factors in Solanum tuberosum. Chin J Appl Environ Biol, 2013, 19 (2): 205-214]
25 Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families database [J]. Nucleic Acids Res, 2008, 36: D281-288
26 HMMER 3.0 [EB/OL]. http://hmmer.janelia.org/
27 Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: identification of signaling domains [J]. Proc Natl Acad Sci USA, 1998, 95 (11): 5857-5864
28 Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X [J]. Trends Biochem Sci, 1998, 23 (10): 403-405
29 Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, andmaximum parsimony methods [J]. Mol Biol Evol, 2011, 28 (10): 2731-2739
30 Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. TM4 microarray software suite [J]. Methods Enzymol, 2006, 411: 134-193
31 Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR [J]. Nucleic Acids Res, 2002, 30 (9): e36

相似文献/References:

[1]葛体达,黄丹枫** 芦波 唐东梅 宋世威.无机氮和有机氮对水培番茄幼苗碳水化合物积累及氮素吸收的影响*[J].应用与环境生物学报,2008,14(05):604.
[2]张春梅,邹志荣,张志新,等.外源亚精胺对模拟干旱胁迫下番茄幼苗活性氧水平和抗氧化系统的影响[J].应用与环境生物学报,2009,15(03):301.[doi:10.3724/SP.J.1145.2009.00301]
 ZHANG Chunmei,ZOU Zhirong,ZHANG Zhixin,et al.Effects of Exogenous Spermidine on Reactive Oxygen Levels and Antioxidative System of Tomato Seedling under Polyethlene Glycol Stress[J].Chinese Journal of Applied & Environmental Biology,2009,15(05):301.[doi:10.3724/SP.J.1145.2009.00301]
[3]刘继恺,高永峰,牛向丽,等.番茄HP1和HP2基因RNA共干涉载体的构建及遗传转化[J].应用与环境生物学报,2009,15(05):591.[doi:10.3724/SP.J.1145.2009.00591]
 LIU Jikai,GAO Yongfeng,NIU Xiangli & LIU Yongsheng.Construction and Transformation of Co-RNAi Vector of Tomato HP1 and HP2 Genes[J].Chinese Journal of Applied & Environmental Biology,2009,15(05):591.[doi:10.3724/SP.J.1145.2009.00591]
[4]崔向超,胡君利,林先贵,等.丛枝菌根真菌与复硝酚钠在番茄育苗中的应用[J].应用与环境生物学报,2012,18(05):843.[doi:10.3724/SP.J.1145.2012.00843]
 CUI Xiangchao,HU Junli,LIN Xiangui,et al.Application of Arbuscular Mycorrhizal Fungi and Compound Sodium Nitrophenolate in Tomato Seedling Growth[J].Chinese Journal of Applied & Environmental Biology,2012,18(05):843.[doi:10.3724/SP.J.1145.2012.00843]
[5]张治国,高永峰,苗敏,等.番茄SlWD1基因的克隆及SlWD1与DDB1的相互作用[J].应用与环境生物学报,2013,19(04):623.[doi:10.3724/SP.J.1145.2013.00623]
 ZHANG Zhiguo,GAO Yongfeng,MIAO Min,et al.Cloning of SlWD1 Gene and Interaction of SlWD1 with DDB1 in Tomato[J].Chinese Journal of Applied & Environmental Biology,2013,19(05):623.[doi:10.3724/SP.J.1145.2013.00623]
[6]张俊芳,唐晓凤,李欲翔,等.番茄SIZ1-like1基因的克隆与功能[J].应用与环境生物学报,2015,21(03):406.[doi:10.3724/SP.J.1145.2014.12016]
 ZHANG Junfang,TANG Xiaofeng,LI Yuxiang,et al.Cloning and function study of tomato SUMO E3 ligase SIZ1-like1 gene[J].Chinese Journal of Applied & Environmental Biology,2015,21(05):406.[doi:10.3724/SP.J.1145.2014.12016]
[7]杨述章,高兰阳,孙晓春,等.过量表达SlWD6基因增强番茄抗旱和耐盐功能[J].应用与环境生物学报,2015,21(03):413.[doi:10.3724/SP.J.1145.2015.01006]
 YANG Shuzhang,GAO Lanyang,SUN Xiaochun,et al.Over-expressing SlWD6 gene to improve drought and salt tolerance of tomato[J].Chinese Journal of Applied & Environmental Biology,2015,21(05):413.[doi:10.3724/SP.J.1145.2015.01006]
[8]郑娜,柯林峰,杨景艳,等.来源于污染土壤的植物根际细菌对番茄幼苗的促生与盐耐受机制[J].应用与环境生物学报,2018,24(01):47.[doi:10.19675/j.cnki.1006-687x.2017.03031]
 ZHENG Na,KE Linfeng,YANG Jingyan,et al.Growth improvement and salt tolerance mechanisms of tomato seedlings mediated by plant growth-promoting rhizobacteria from contaminated soils[J].Chinese Journal of Applied & Environmental Biology,2018,24(05):47.[doi:10.19675/j.cnki.1006-687x.2017.03031]
[9]孙德智,韩晓日,彭靖,等.外源NO和水杨酸对盐胁迫下番茄幼苗光合机构的保护作用[J].应用与环境生物学报,2018,24(03):457.[doi:10.19675/j.cnki.1006-687x.2017.08019]
 SUN Dezhi**,HAN Xiaori,PENG Jing,et al.Protective effect of exogenous nitric oxide and salicylic acid on the photosynthetic apparatus of tomato seedling leaves under NaCl stress[J].Chinese Journal of Applied & Environmental Biology,2018,24(05):457.[doi:10.19675/j.cnki.1006-687x.2017.08019]
[10]于丰源 蒋礼玲 ** 贾举庆 张真真 陈思佳 牛向丽 王明雪 黄胜雄**.中华猕猴桃bZIP家族成员的比较基因组学分析*[J].应用与环境生物学报,2020,26(02):1.[doi:10.19675/j.cnki.1006-687x.2019.06032]
 Fengyuan YU,Liling JIANG **,et al.Comparative genomics analyses of bZIP family members in Actinidia chinensis*[J].Chinese Journal of Applied & Environmental Biology,2020,26(05):1.[doi:10.19675/j.cnki.1006-687x.2019.06032]

备注/Memo

备注/Memo:
国家自然科学基金项目(31171179)、中国博士后科学基金面上项目(2013M541824)和中央高校基本科研业务费专项资金(2012HGQC0018,2013HGBZ0168)资助 Supported by the National Natural Science Foundation of China (31171179), the China Postdoctoral Science Foundation (2013M541824) and the Fundamental Research Funds for the Central Universities (2012HGQC0018, 2013HGBZ0168)
更新日期/Last Update: 2014-10-23