小桐子bZIP转录因子的全基因组鉴定及表达分析

doi:10.7668/hbnxb.201750960

摘要/Abstract

摘要： 为明确小桐子bZIP转录因子家族的结构特征以及其在植物响应生物与非生物胁迫中的作用，利用生物信息学方法，从全基因组水平鉴定小桐子bZIP转录因子家族，并对其基因结构、进化关系、染色体定位、共线性关系及组织与低温表达特性进行分析。结果表明，共鉴定到51个小桐子bZIP基因，系统进化树分析将其分为10个亚族（A-I及S）。基因定位显示，51个小桐子bZIP基因不均匀地分布于11条染色体，其中2号与4号染色体鉴定到基因的串联复制。基因结构分析表明，小桐子bZIP基因包含1~13个外显子，其中，S亚族基因包含1~2个外显子，而G亚族基因包含12~13个外显子。bZIP转录因子主要定位在细胞核，氨基酸数目为113~768个，等电点4.70~10.30。启动子顺式作用元件鉴定发现3~27个响应激素如赤霉素、脱落酸、乙烯及生长素与非生物胁迫如低温、高温及创伤等调控元件。转录组表达分析显示，小桐子bZIP基因具有器官表达特异性，26个bZIP基因在叶片、根及种子中均有表达，其他基因仅在特定器官中表达。同时，鉴定到14个小桐子bZIP基因在低温条件下上调表达。在叶片中，qRT-PCR试验显示JcbZIP3与JcbZIP14表达量在低温处理24 h时上调达到显著水平，与小桐子抗冷性的形成及低温信号转导过程直接相关。研究结果为小桐子bZIP基因的克隆与调控机制研究奠定了基础。

关键词: 小桐子, 转录因子, bZIP, 基因家族, 表达分析

Abstract: The purpose of the study was to further understand the structure characteristics of Basic leucine zipper (bZIPs) and its function in response to biotic and abiotic stress. Based on the Jatropha curcas genome and bioinformatics methods, bZIP family genes from J.curcas were identified, and then the gene structure, phylogentic relationship, chromosomal location, synteny relationship, as well as organ and chilling hardening expression, were systematically analyzed. The results showed that a total of 51 bZIP genes were systematically identified from J.curcas genome and classified into 10 subfamilies (A-I and S) according to phylogentic relationship. Chromosome mapping analysis indicated that J.curcas bZIP genes were distributed with different densities on 11 chromosomes, and tandem duplications were found on chromosome No.2 and 4, which was the main power for the expansion of J.curcas bZIP gene family. The results of gene structure analysis revealed that most of the J.curcas bZIP gene contained 1-13 exons, and the member of subfamilies of S and G owned 1-2 and 12-13 exons, respectively. Subcellular localization showed that the predicted bZIP proteins mainly located in nucleus with amino acid number ranged from 113 to 768 aa and pI value distributed from 4.70 to 10.30. 3-27 hormonal response elements for gibberellin, abscisic acid, ethylene, auxin and abiotic stress response elements like low temperature, heat and wound were identified in the promoter of J.curcas bZIP genes. Transcriptome expression analysis showed that J.curcas bZIP genes exhibited different tissue-specific expression patterns, and 26 J.curcas bZIP genes were found to be expressed in the detected organs of leaves, roots, and seeds, while the others were expressed in the specific organ tissues. Moreover, the expression profiling of 14 J.curcas bZIP genes were up-regulated under chilling hardening. In leaves, JcbZIP3 and JcbZIP14 reached to the highest expression levels after 24 h chilling hardening based on the qRT-PCR results, which were associated with the events of chilling resistance formation and cold signalling transduction. These results were helpful for the cloning and regulation mechanism analysis of bZIP genes in J.curcas.

Key words: Jatropha curcas, Transcription factor, bZIP, Gene family, Expression analysis

中图分类号:

Q78
S794.03

王海波, 郭俊云, 唐利洲, 刘潮. 小桐子bZIP转录因子的全基因组鉴定及表达分析[J]. 华北农学报, 2019, 34(2): 44-58. doi: 10.7668/hbnxb.201750960.

WANG Haibo, GUO Junyun, TANG Lizhou, LIU Chao. Genome-wide Identification and Expression Analysis of bZIP Transcription Factor Family in Jatropha curcas[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(2): 44-58. doi: 10.7668/hbnxb.201750960.

http://www.hbnxb.net/CN/Y2019/V34/I2/44

参考文献

[1] Nakashima K, Ito Y, Yamaguchi-Shinozaki K. Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses[J]. Plant Physiology, 2009, 149(1):88-95.doi:10.1104/pp.108.129791.
[2] Amorim L L B, da Fonseca Dos Santos R, Neto J P B, Guida-Santos M, Crovella S, Benko-Iseppon A M. Transcription factors involved in plant resistance to pathogens[J]. Current Protein & Peptide Science, 2017, 18(4):335-351.doi:10.2174/1389203717666160619185308.
[3] Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F. bZIP transcription factors in Arabidopsis[J]. Trends in Plant Science, 2002, 7(3):106-111.doi:10.1016/S1360-1385(01)02223-3.
[4] Nijhawan A, Jain M, Tyagi A K, Khurana J P. Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice[J]. Plant Physiology, 2008, 146(2):333-350.doi:10.1104/pp.107.112821.
[5] Wei K F, Chen J, Wang Y M, Chen Y H, Chen S X, Lin Y N, Pan S, Zhong X J, Xie D X. Genome-wide analysis of bZIP-encoding genes in maize[J]. DNA Research:an International Journal for Rapid Publication of Reports on Genes and Genomes, 2012, 19(6):463-476.doi:10.1093/dnares/dss026.
[6] Banerjee A, Roychoudhury A. Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress[J]. Protoplasma, 2017, 254(1):3-16.doi:10.1007/s00709-015-0920-4.
[7] E Z G, Zhang Y P, Zhou J H, Wang L. Mini review roles of the bZIP gene family in rice[J]. Genetics and Molecular Research, 2014, 13(2):3025-3036.doi:10.4238/2014.April.16.11.
[8] Noman A, Liu Z P, Aqeel M, Zainab M, Khan M I, Hussain A, Ashraf M F, Li X, Weng Y H, He S L. Basic leucine zipper domain transcription factors:the vanguards in plant immunity[J]. Biotechnology Letters, 2017, 39(12):1779-1791.doi:10.1007/s10529-017-2431-1.
[9] Zhang M, Liu Y H, Shi H, Guo M L, Chai M N, He Q, Yan M K, Cao D, Zhao L H, Cai H Y, Qin Y. Evolutionary and expression analyses of soybean basic leucine zipper transcription factor family[J]. BMC Genomics, 2018, 19(1):159.doi:10.1186/s12864-018-4511-6.
[10] Wang J Z, Zhou J X, Zhang B L, Vanitha J, Ramachandran S, Jiang S Y. Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum[J]. Journal of Integrative Plant Biology, 2011, 53(3):212-231.doi:10.1111/j.1744-7909.2010.01017.x.
[11] Liu J Y, Chen N N, Chen F, Cai B, Dal Santo S, Tornielli G B, Pezzotti M, Cheng Z M. Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera)[J]. BMC Genomics, 2014, 15(8):281.doi:10.1186/1471-2164-15-281.
[12] 张珍珠, 陈秀玲, 王沛文, 戚飞, 谢莹, 王傲雪. 番茄bZIP基因家族的系统进化分析[J]. 东北农业大学学报, 2014, 45(9):47-55.doi:10.3969/j.issn.1005-9369.2014.09.007.s.
Zhang Z Z, Chen X L, Wang P W, Qi F, Xie Y, Wang A X. Phyletic evolution analysis of bZIP family in tomato[J]. Journal of Northeast Agricultural University, 2014, 45(9):47-55.
[13] 孙明岳, 周君, 谭秋平, 付喜玲, 陈修德, 李玲, 高东升. 苹果bZIP转录因子家族生物信息学分析及其在休眠芽中的表达[J]. 中国农业科学, 2016, 49(7):1325-1345.doi:10.3864/j.issn.0578-1752. 2016.07.010.
Sun M Y, Zhou J, Tan Q P, Fu X L, Chen X D, Li L, Gao D S. Analysis of basic leucine zipper genes and their expression during bud dormancy in apple (Malus×domestica)[J]. Scientia Agricultural Sinica, 2016, 49(7):1325-1345.
[14] Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shini T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena J A, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.[J]. DNA Research:an International Journal for Rapid Publication of Reports on Genes and Genomes, 2011, 18(1):65-76.doi:10.1093/dnares/dsq030.
[15] Wu P Z, Zhou C P, Cheng S F, Wu Z Y, Lu W J, Han J L, Chen Y B, Chen Y, Ni P X, Wang Y, Xu X, Huang Y, Song C, Wang Z W, Shi N, Zhang X D, Fang X H, Yang Q, Jiang H W, Chen Y P, Li M R, Wang Y, Chen F, Wang J, Wu G J. Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant[J]. The Plant Journal:for Cell and Molecular Biology, 2015, 81(5):810-821.doi:10.1111/tpj.12761.
[16] Suyama M, Torrents D, Bork P. PAL2NAL:robust conversion of protein sequence alignments into the corresponding codon alignments[J]. Nucleic Acids Research, 2006, 34(SI):W609-W612.doi:10.1093/nar/gkl315.
[17] Wang H B, Zou Z R, Wang S S, Gong M. Deep sequencing-based transcriptome analysis of the oil-bearing plant Physic Nut (Jatropha curcas L.) under cold treatments[J]. Plant Omics, 2014, 7(3):178-187.
[18] Wang H B, Zou Z R, Wang S S, Gong M. Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.[J]. PLoS One, 2013, 8(12):e82817.doi:10.1371/journal.pone.0082817.
[19] tHoen P A, Ariyurek Y, Thygesen H H, Vreugdenhil E, Vossen R H, de Menezes R X, Boer J M, van Ommen G J, den Dunnen J T. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms[J]. Nucleic Acids Research, 2008, 36(21):e141.doi:10.1093/nar/gkn705.
[20] Morrissy A S, Morin R D, Delaney A, Zeng T, McDonald H, Jones S, Zhao Y, Hirst M, Marra M A. Next-generation tag sequencing for cancer gene expression profiling[J]. Genome Research, 2009, 19(10):1825-1835.doi:10.1101/gr.094482.109.
[21] Bai Y L, Zhu W B, Hu X C, Sun C C, Li Y L, Wang D D, Wang Q H, Pei G L, Zhang Y F, Guo A G, Zhao H X, Lu H B, Mu X Q, Hu J J, Zhou X N, Xie C G. Genome-wide analysis of the bZIP gene family identifies two ABI5-Like bZIP transcription factors, BrABI5a and BrABI5b, as positive modulators of ABA signalling in Chinese cabbage[J]. PLoS One, 2016, 11(7):e0158966.doi:10.1371/journal.pone.0158966.
[22] Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions[J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(21):11632-11637.doi:10.1073/pnas.190309197.
[23] Finkelstein R R, Lynch T J. The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor[J]. The Plant Cell, 2000, 12(4):599-609.doi:10.2307/3871072.
[24] Liu J X, Srivastava R, Howell S H. Stress-induced expression of an activated form of AtbZIP17 provides protection from salt stress in Arabidopsis[J]. Plant, Cell & Environment, 2008, 31(12):1735-1743.doi:10.1111/j.1365-3040.2008.01873.x.
[25] Srivastava R, Deng Y, Shah S, Rao A G, Howell S H. BINDING PROTEIN is a master regulator of the endoplasmic reticulum stress sensor/transducer bZIP28 in Arabidopsis[J]. Plant Cell, 2013, 25(4):1416-1429.doi:10.1105/tpc.113.110684.
[26] Liu J X, Srivastava R, Che P, Howell S H. An endoplasmic reticulum stress response in Arabidopsis is mediated by proteolytic processing and nuclear relocation of a membrane-associated transcription factor, bZIP28[J]. Plant Cell, 2007, 19(12):4111-4119.doi:10.1105/tpc.106.050021.
[27] Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H Y, Lee I, Deng X W. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development[J]. Plant Cell, 2007, 19(3):731-749.doi:10.1105/tpc.106.047688.
[28] Zhang Y Q, Zheng S, Liu Z J, Wang L G, Bi Y R. Both HY5 and HYH are necessary regulators for low temperature-induced anthocyanin accumulation in Arabidopsis seedlings[J]. Journal of Plant Physiology, 2011, 168(4):367-374.doi:10.1016/j.jplph.2010.07.025.
[29] Singh A, Ram H, Abbas N, Chattopadhyay S. Molecular interactions of GBF1 with HY5 and HYH proteins during light-mediated seedling development in Arabidopsis thaliana[J]. The Journal of Biological Chemistry, 2012, 287(31):25995-26009.doi:10.1074/jbc.M111.333906.
[30] Gangappa S N, Botto J F. The multifaceted roles of HY5 in plant growth and development[J]. Molecular Plant, 2016, 9(10):1353-1365.doi:10.1016/j.molp.2016.07.002.
[31] Kusano T, Berberich T, Harada M, Suzuki N, Sugawara K. A maize DNA-binding factor with a bZIP motif is induced by low temperature[J]. Molecular & General Genetics, 1995, 248(5):507-517.doi:10.1007/bf02423445.
[32] Izawa T, Foster R, Chua N H. Plant bZIP protein DNA binding specificity[J]. Journal of Molecular Biology, 1993, 230(4):1131-1144.doi:10.1006/jmbi.1993.1230.
[33] Schindler U, Beckmann H, Cashmore A R. TGA1 and G-box binding factors:two distinct classes of Arabidopsis leucine zipper protiens compete for the G-box-like element TGACGTGG[J]. Plant Cell, 1992, 4(10):1309-1319.doi:10.2307/3869416.
[34] Zhang Y L, Tessaro M J, Lassner M, Li X. Knockout analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance[J]. Plant Cell, 2003, 15(11):2647-2653.doi:10.1105/tpc.014894.
[35] Miao Z H, Liu X, Lam E. TGA3 is a distinct member of the TGA family of bZIP transcription factors in Arabidopsis thaliana[J]. Plant Molecular Biology, 1994, 25(1):1-11.doi:10.1007/bf00024193.
[36] Foley R C, Singh K B. TGA5 acts as a positive and TGA4 acts as a negative regulator of ocs element activity in Arabidopsis roots in response to defence signals[J]. FEBS Letters, 2004, 563(1/3):141-145.doi:10.1016/S0014-5793(04)00288-1.
[37] Mallappa C, Yadav V, Negi P, Chattopadhyay S. A basic leucine zipper transcription factor, G-box-binding factor 1, regulates blue light-mediated photomorphogenic growth in Arabidopsis[J]. The Journal of Biological Chemistry, 2006, 281(31):22190-22199.doi:10.1074/jbc.M601172200.
[38] Terzaghi W B, Bertekap R L Jr, Cashmore A R. Intracellular localization of GBF proteins and blue light-induced import of GBF2 fusion proteins into the nucleus of cultured Arabidopsis and soybean cells[J]. The Plant Journal:for Cell and Molecular Biology, 1997, 11(5):967-982.doi:10.1046/j.1365-313X. 1997.11050967.x.
[39] Menkens A E, Schindler U, Cashmore A R. The G-box:a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins[J]. Trends in Biochemical Sciences, 1995, 20(12):506-510.doi:10.1016/S0968-0004(00)89118-5.

选择文件类型/文献管理软件名称

选择包含的内容