[1]李元元,高志强,曹清河.甘薯SPF1转录因子的生物信息学分析[J].江苏农业学报,2017,(04):760-767.[doi:doi:10.3969/j.issn.1000-4440.2017.04.006]
 LI Yuan-yuan,GAO Zhi-qiang,CAO Qing-he.Bioinformatics analysis of SPF1 transcription factors from sweet potato[Ipomoea batatas(L.) Lam][J].,2017,(04):760-767.[doi:doi:10.3969/j.issn.1000-4440.2017.04.006]
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甘薯SPF1转录因子的生物信息学分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2017年04期
页码:
760-767
栏目:
遗传育种·生理生化
出版日期:
2017-08-30

文章信息/Info

Title:
Bioinformatics analysis of SPF1 transcription factors from sweet potato[Ipomoea batatas(L.) Lam]
作者:
李元元1高志强2曹清河1
(1.江苏省徐州市农业科学院,江苏徐州221121;2.江苏师范大学药用植物生物技术省级重点实验室,江苏徐州221116)
Author(s):
LI Yuan-yuan1GAO Zhi-qiang2CAO Qing-he1
(1.Institute of Agricultural Sciences of Xuzhou, Xuzhou 221121, China;2.The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, China)
关键词:
甘薯SPF1转录因子WRKY结构域
Keywords:
sweet potatoSPF1transcription factorWRKY domain
分类号:
S531.032
DOI:
doi:10.3969/j.issn.1000-4440.2017.04.006
文献标志码:
A
摘要:
WRKY蛋白是一类植物特有的转录因子超家族,SPF1是第一个从植物(高系14)中克隆的WRKY家族基因。借助生物信息学手段,对甘薯SPF1蛋白组成、结构和功能进行分析预测。结果表明,SPF1编码蛋白含有丰富的丝氨酸位点,并含有2个WRKY保守结构域,分别带有CX4CX22HXH和CX4CX23HXH锌指结构,分别形成4个和5个β-折叠片。SPF1和甘薯祖先种Ipomoea trifida WRKY结构域均具有非常保守的WRKYG(Q/K)K氨基酸序列,并且C端WRKY结构域的保守性比N端WRKY结构域的低。系统进化树分析结果显示,蛋白N端和C端的WRKY结构域分属2个不同的分支。蛋白结构预测结果显示,SPF1 WRKY结构区(204~445 aa)处于蛋白三维结构的内侧,形成非亲水性靶标DNA结合区。SPF1作为转录因子,在调控细胞核基因表达的同时,其蛋白N端序列具有叶绿体定位功能。推测SPF1可能参与细胞核和叶绿体的基因表达调控。
Abstract:
WRKY protein is a kind of plant specific transcription factor superfamily, and SPF1 is the first cloned WRKY gene from sweet potato (Kokei No.14). Using Bioinformatics tools, the protein structure and function of SPF1 were analyzed. SPF1 protein is rich in serine amino acids and contains two WRKY domains harbouring CX4CX22HXH and CX4CX23HXH zinc finger structures respectively, finally forming four and five β-sheets. The WRKY domains in SPF1 of Kokei No.14 and sweet potato ancestor Ipomoea trifida had highly conservative WRKYG (Q/K) K amino acid sequence, and C terminus presented relatively lower conservation than N terminus did. Phylogenetic analysis revealed that the WRKY domain in termini N and C belonged to two different branches. The two WRKY domains(204~445 aa) in SPF1 were located inside of the protein three-dimensional structure where the non-hydrophilic target DNA was bound. As a transcription factor, SPF1 might be involved in the regulations of nuclear and chloroplast genes expression.

参考文献/References:

[1]FAOSTAT. Food and agriculture organization of the United Nations, production statistics[EB/OL].
[2016-12-16].http://faostat3.fao.org/home/index.html.
[2]GU Y H, TAO X, LAI X J, et al. Exploring the polyadenylated RNA virome of sweet potato through high-throughput sequencing[J]. PloS One, 2014, 9(6): e98884.
[3]YAN L, LAI X, LI X, et al. Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata][J]. PloS One, 2015, 10(4): e0124083.
[4]BOETTCHER M, MCMANUS M T. Choosing the right tool for the job: RNAi, TALEN, or CRISPR[J]. Molecular Cell, 2015, 58(4): 575-585.
[5]PHUKAN U J, JEENA G S, SHUKLA R K. WRKY transcription factors: molecular regulation and stress responses in plants[J]. Frontiers in Plant Science, 2016, 7:760.
[6] LI W, WANG H, YU D. Arabidopsis WRKY transcription factors WRKY12 and WRKY13 oppositely regulate flowering under short-day conditions[J]. Molecular Plant, 2016, 9(11): 1492-1503.
[7]CAI Y, CHEN X, XIE K, et al. Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice[J]. PLoS One, 2014, 9(7): e102529.
[8]DING Z J, YAN J Y, LI C X, et al. Transcription factor WRKY46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis[J]. The Plant Journal, 2015, 84(1): 56-69.
[9]RISHMAWI L, PESCH M, JUENGST C, et al. Non-cell-autonomous regulation of root hair patterning genes by WRKY75 in Arabidopsis[J]. Plant Physiology, 2014, 165(1): 186-195.
[10]THOMAS H, OUGHAM H. The stay-green trait[J]. Journal of Experimental Botany, 2014, 65(14): 3889-3900.
[11]HAN M, KIM C Y, LEE J, et al. OsWRKY42 represses OsMT1d and induces reactive oxygen species and leaf senescence in rice[J]. Molecules and Cells, 2014, 37(7): 532-539.
[12]DAI X, WANG Y, ZHANG W H. OsWRKY74, a WRKY transcription factor, modulates tolerance to phosphate starvation in rice[J]. Journal of Experimental Botany, 2016, 67(3):947-960.
[13]SU T, XU Q, ZHANG F C, et al. WRKY42 modulates phosphate homeostasis through regulating phosphate translocation and acquisition in Arabidopsis[J]. Plant Physiology, 2015, 167(4): 1579-1591.
[14]YAN J Y, LI C X, SUN L, et al. A WRKY transcription factor regulates Fe translocation under Fe deficiency[J]. Plant Physiology, 2016, 171(3): 2017-2027.
[15]YAMADA Y, SATO F. Tyrosine phosphorylation and protein degradation control the transcriptional activity of WRKY involved in benzylisoquinoline alkaloid biosynthesis[J]. Scientific Reports, 2016, 6:31988.
[16]SHEN Q H, SAIJO Y, MAUCH S, et al. Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses[J]. Science, 2007, 315(5815): 1098-1103.
[17]LE ROUX C, HUET G, JAUNEAU A, et al. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity[J]. Cell, 2015, 161(5): 1074-1088.
[18]HIRAKAWA H, OKADA Y, TABUCHI H, et al. Survey of genome sequences in a wild sweet potato, Ipomoea trifida (HBK) G. Don[J]. DNA Research, 2015, 22(2):171-179.
[19]ISHIGURO S, NAKAMURA K. Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5′ upstream regions of genes coding for sporamin and β-amylase from sweet potato[J]. Molecular and General Genetics MGG, 1994, 244(6): 563-571.
[20]JIN J, TIAN F, YANG D C, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants[J]. Nucleic Acids Research, 2017, 45: D1040-D1045.
[21]MARCHLER-BAUER A, DERBYSHIRE M K, GONZALES N R, et al. CDD: NCBI′s conserved domain database[J]. Nucleic Acids Research, 2014: gku1221.
[22]DE CASTRO E, SIGRIST C J A, GATTIKER A, et al. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins[J]. Nucleic Acids Research, 2006, 34: W362-W365.
[23]CROOKS G E, HON G, CHANDONIA J M, et al. WebLogo: a sequence logo generator[J]. Genome Research, 2004, 14(6): 1188-1190.
[24]SAITOU N, NEI M. The neighbor-joining method: a new method for reconstructing phylogenetic trees[J]. Molecular Biology and Evolution, 1987, 4(4): 406-425.
[25]KUMAR S, STECHER G, TAMURA K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 2016, 33:1870-1874.
[26]NEI M, KUMAR S. Molecular evolution and phylogenetics[M]. United Kingdom: Oxford University Press, 2000.
[27]FELSENSTEIN J. Confidence limits on phylogenies: an approach using the bootstrap[J]. Evolution, 1985, 39:783-791.
[28]LIU X, WU J, WANG J, et al. WebLab: a data-centric, knowledge-sharing bioinformatic platform[J]. Nucleic Acids Research, 2009, 37(suppl 2): W33-W39.
[29]OBENAUER J C, CANTLEY L C, YAFFE M B. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs[J]. Nucleic Acids Research, 2003, 31(13): 3635-3641.
[30]YACHDAV G, KLOPPMANN E, KAJAN L, et al. PredictProtein—an open resource for online prediction of protein structural and functional features[J]. Nucleic Acids Research, 2014, 42(W1):W337-W343.
[31]GUEX N, PEITSCH M C. SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling[J]. Electrophoresis, 1997, 18(15): 2714-2723.
[32] SZKLARCZYK D, SANTOS A, VON MERING C, et al. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data[J]. Nucleic Acids Research, 2016, 44(D1):D380-D384.
[33]SZKLARCZYK D, FRANCESCHINI A, WYDER S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life[J]. Nucleic Acids Research, 2015, 43(D1):D447-D452.
[34]WU K L, GUO Z J, WANG H H, et al. The WRKY family of transcription factors in rice and Arabidopsis and their origins[J]. DNA Research, 2005, 12(1): 9-26.
[35]TRIPATHI P, RABARA R C, LANGUM T J, et al. The WRKY transcription factor family in Brachypodium distachyon[J]. Bmc Genomics, 2012, 13: 270.
[36]HUANG X, LI K, XU X, et al. Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress[J]. BMC Genomics, 2015, 16: 1104.
[37]LI M Y, XU Z S, TIAN C, et al. Genomic identification of WRKY transcription factors in carrot (Daucus carota) and analysis of evolution and homologous groups for plants[J]. Scientific Reports, 2016, 6:23101.
[38]SONG H, WANG P, LIN J Y, et al. Genome-wide identification and characterization of WRKY gene family in peanut[J]. Frontiers in Plant Science, 2016, 7:534.
[39]CHI Y, YANG Y, ZHOU Y, et al. Protein–protein interactions in the regulation of WRKY transcription factors[J]. Molecular Plant, 2013, 6(2): 287-300.
[40]ISHIHAMA N, ADACHI H, YOSHIOKA M, et al. In vivo phosphorylation of WRKY transcription factor by MAPK[J]. Plant MAP Kinases: Methods and Protocols, 2014, 1171:171-181.
[41]CHANG I F, CURRAN A, WOOLSEY R, et al. Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana[J]. Proteomics, 2009, 9(11): 2967-2985.

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备注/Memo

备注/Memo:
收稿日期:2016-12-31 基金项目:徐州市农业科学院科研基金项目(2015005) 作者简介:李元元(1986-),女,江苏沛县人,硕士,助理研究员,研究方向为植物生物技术。(Tel)0516-82189590;(E-mail)li_yy2016@126.com
更新日期/Last Update: 2017-09-01