Analysis of Brassica rapa ESTs: Gene discovery and expression patterns of AP2/ERF family genes

Molecular Biology Reports

Volumn 37, Issue 5, 2010, Pages 2485-2492

  Zhuang, Jing ^a,c   Xiong, Ai Sheng ^a   Peng, Ri He ^a   Gao, Feng ^a   Zhu, Bo ^a   Zhang, Jian ^c   Fu, Xiao Yan ^a   Jin, Xiao Feng ^a   Chen, Jian Min ^d   Zhang, Zhen ^b   Qiao, Yu Shan ^b   Yao, Quan Hong ^a  

^a INSTITUTE OF EDIBLE FUNGI   (China)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

^c ALBERTA RESEARCH COUNCIL   (Canada)

^d YANGZHOU UNIVERSITY   (China)

Author keywords

AP2 ERF; Arabidopsis thaliana; Brassica rapa; Expression pattern; Transcription factor

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP2; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE ISOLATION; GENE LOCATION; GENE NUMBER; GENETIC TRANSCRIPTION; MOLECULAR BIOLOGY; MOLECULAR CLONING; PLANT LEAF; PLANT ROOT; PLANT SEED; PLANT TISSUE; SEQUENCE DATABASE; TISSUE DISTRIBUTION; TURNIP;

AMINO ACID SEQUENCE; ARABIDOPSIS; BRASSICA RAPA; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; ORGAN SPECIFICITY; PHYLOGENY; PLANT PROTEINS; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

ARABIDOPSIS THALIANA; BRASSICA RAPA; BRASSICA RAPA SUBSP. PEKINENSIS;

EID: 77955658331     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-009-9763-4     Document Type: Article

References (32)

1. W Wang B Vinocur A Altman 2003 Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance Planta 218 1 14 10.1007/s00425-003-1105-5 1:CAS:528:DC%2BD3sXovV2ltbo%3D 14513379 (Pubitemid 38097908)
2. D Kizis V Lumbreras M Pagès 2001 Role of AP2/EREBP transcription factors in gene regulation during abiotic stress FEBS Lett 498 187 189 10.1016/S0014-5793(01)02460-7 1:CAS:528:DC%2BD3MXksVGlu7g%3D 11412854 (Pubitemid 32539200)
3. SK Yamaguchi K Shinozaki 2006 Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses Annu Rev Plant Biol 57 781 803 10.1146/annurev.arplant.57.032905.105444 (Pubitemid 44061045)
4. JL Riechmann EM Meyerowitz 1998 The AP2/EREBP family of plant transcription factors Biol Chem 379 633 646 10.1515/bchm.1998.379.6.633 1:CAS:528:DyaK1cXksF2qs7Y%3D 9687012
5. SR Wessler 2005 Homing into the origin of the AP2 DNA binding domain Trends Plant Sci 10 54 56 10.1016/j.tplants.2004.12.007 1:CAS:528: DC%2BD2MXhtlajtro%3D 15708341 (Pubitemid 40234479)
6. JG Dubouzet Y Sakuma Y Ito M Kasuga EG Dubouzet S Miura M Seki K Shinozaki SK Yamaguchi 2003 OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression Plant J 33 751 763 10.1046/j.1365-313X.2003. 01661.x 1:CAS:528:DC%2BD3sXislWiu7w%3D 12609047 (Pubitemid 36325917)
7. XY Fu Z Zhang RH Peng AS Xiong JG Liu LJ Wu F Gao H Zhu ZK Guo QH Yao 2007 Isolation and characterization of a novel cDNA encoding ERF/AP2-type transcription factor OsAP25 from Oryza sativa L Biotechnol Lett 29 1293 1299 10.1007/s10529-007-9370-1 1:CAS:528:DC%2BD2sXnt1Kitb4%3D 17516027 (Pubitemid 47035010)
8. TW Yang LJ Zhang TG Zhang H Zhang SJ Xu LZ An 2005 Transcriptional regulation network of cold-responsive genes in higher plants Plant Sci 169 987 995 10.1016/j.plantsci.2005.07.005 1:CAS:528:DC%2BD2MXhtVyntrjL (Pubitemid 41425690)
9. QL Qin JG Liu Z Zhang RH Peng AS Xiong QH Yao JM Chen 2007 Isolation, optimization, and functional analysis of the cDNA encoding transcription factor RdreB1 in Oryza Sativa L Mol Breed 19 329 340 10.1007/s11032-006-9065-7 1:CAS:528:DC%2BD2sXjtFyht7o%3D (Pubitemid 46440194)
10. N Gutterson TL Reuber 2004 Regulation of disease resistance pathways by AP2/ERF transcription factors Curr Opin Plant Biol 7 465 471 10.1016/j.pbi.2004.04.007 1:CAS:528:DC%2BD2cXlsVWhurg%3D 15231271 (Pubitemid 38871622)
11. RC Elliott AS Betzner E Huttner MP Oakes WQ Tucker D Gerentes P Perez DR Smyth 1996 AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth Plant Cell 8 155 168 10.1105/tpc.8.2.155 1:CAS:528:DyaK28XhtlKqsbk%3D 8742707 (Pubitemid 3035453)
12. Y Sakuma Q Liu JG Dubouzet H Abe K Shinozaki SK Yamaguchi 2002 DNA- binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression Biochem Biophys Res Commun 290 998 1009 10.1006/bbrc.2001.6299 1:CAS:528: DC%2BD38XksVyquw%3D%3D 11798174 (Pubitemid 34687462)
13. T Nakano K Suzuki T Fujimura H Shinshi 2006 Genome-wide analysis of the ERF gene family in Arabidopsis and rice Plant Physiol 140 411 432 10.1104/pp.105.073783 1:CAS:528:DC%2BD28XjsV2itLk%3D 16407444 (Pubitemid 43956266)
14. O Jaillon JM Aury B Noel A Policriti C Clepet A Casagrande N Choisne S Aubourg 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 463 467 10.1038/nature06148 1:CAS:528:DC%2BD2sXhtV2is7%2FF 17721507 (Pubitemid 47509545)
15. J Zhuang B Cai RH Peng B Zhu XF Jin Y Xue F Gao XY Fu YS Tian W Zhao YS Qiao Z Zhang AS Xiong QH Yao 2008 Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa Biochem Biophys Res Commun 371 468 474 10.1016/j.bbrc.2008.04.087 1:CAS:528:DC%2BD1cXmsVegsrs%3D 18442469
16. MJ Gao G Allard L Byass AM Flanagan J Singh 2002 Regulation and characterization of four CBF transcription factors from Brassica napus Plant Mol Biol 49 459 471 10.1023/A:1015570308704 1:CAS:528:DC%2BD38XkvVWrurw%3D 12090622 (Pubitemid 34622996)
17. TJ Zhao S Sun Y Liu JM Liu Q Liu YB Yan HM Zhou 2006 Regulating the drought-responsive element (DRE)-mediated signaling pathway by synergic functions of trans-active and trans-inactive DRE binding factors in Brassica napus J Biol Chem 281 10752 10759 10.1074/jbc.M510535200 1:CAS:528: DC%2BD28XjsFSqur8%3D 16497677 (Pubitemid 43855497)
18. L Cong TY Chai YX Zhang 2008 Characterization of the novel gene BjDREB1B encoding a DRE-binding transcription factor from Brassica juncea L Biochem Biophys Res Commun 371 702 706 10.1016/j.bbrc.2008.04.126 1:CAS:528: DC%2BD1cXmsFyrtro%3D 18457662
19. JL Riechmann J Heard G Martin L Reuber C Jiang J Keddie L Adam O Pineda OJ Ratcliffe RR Samaha Pilgrim M Creelman P Broun JZ Zhang D Ghandehari BK Sherman G Yu 2000 Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes Science 290 2105 2110 10.1126/science.290.5499.2105 1:CAS:528:DC%2BD3cXptVyjtbk%3D 11118137 (Pubitemid 32001583)
20. QH Zhu AY Guo G Gao YF Zhong M Xu M Huang J Luo 2007 DPTF: a database of poplar transcription factors Bioinformatics 23 1307 1308 10.1093/bioinformatics/ btm113 1:CAS:528:DC%2BD2sXntVOju74%3D 17392330 (Pubitemid 47050553)
21. SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D 9254694 (Pubitemid 27359211)
22. X Huang A Madan 1999 CAP3: a DNA sequence assembly program Genome Res 9 868 877 10.1101/gr.9.9.868 1:CAS:528:DyaK1MXmslKgs7Y%3D 10508846 (Pubitemid 29488446)
23. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: molecular evolutionary genetics analysis MEGA software version 4.0 Mol Biol Evol 24 1596 1599 10.1093/molbev/msm092 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 17488738 (Pubitemid 47236692)
24. E Gasteiger A Gattiker C Hoogland I Ivanyi RD Appel A Bairoch 2003 ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res 31 3784 3788 10.1093/nar/gkg563 1:CAS:528:DC%2BD3sXltVWjtLc%3D 12824418 (Pubitemid 37442246)
25. DL Wilkinson RG Harrison 1991 Predicting the solubility of recombinant proteins in Escherichia coli Biotechnology 9 443 448 10.1038/nbt0591-443 1:CAS:528:DyaK38Xjt1an 1367308
26. GE Crooks G Hon JM Chandonia SE Brenner 2004 WebLogo: a sequence logo generator Genome Res 14 1188 1190 10.1101/gr.849004 1:CAS:528: DC%2BD2cXkvFGht7Y%3D 15173120 (Pubitemid 38811555)
27. HS Cho J Cao JP Ren ED Earle 2001 Control of lepidopteran insect pests in transgenic Chinese cabbage (Brassica rapa ssp. pekinensis) transformed with a synthetic Bacillus thuringiensis cry1C gene Plant Cell Rep 20 1 7 10.1007/s002990000278 1:CAS:528:DC%2BD3MXisFCmtQ%3D%3D (Pubitemid 32375694)
28. H Xu X Wang H Zhao F Liu 2008 An intensive understanding of vacuum infiltration transformation of pakchoi (Brassica rapa ssp. chinensis) Plant Cell Rep 27 1369 1376 10.1007/s00299-008-0564-3 1:CAS:528:DC%2BD1cXotVyksr0%3D 18542966
29. AC Cavell DJ Lydiate IA Parkin C Dean M Trick 1998 Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome Genome 41 62 69 10.1139/gen-41-1-62 1:CAS:528:DyaK1cXisVChu7o%3D 9549059
30. R Schmidt A Acarkan K Boivin 2001 Comparative structural genomics in the Brassicaceae family Plant Physiol Biochem 39 253 262 10.1016/S0981-9428(01) 01239-6 1:CAS:528:DC%2BD3MXjtFajs7g%3D (Pubitemid 32333319)
31. Z Fei X Tang RM Alba JA White CM Ronning GB Martin SD Tanksley JJ Giovannoni 2004 Comprehensive EST analysis of tomato and comparative genomics of fruit ripening Plant J 40 47 59 10.1111/j.1365-313X.2004.02188.x 15361140 (Pubitemid 39342593)
32. P He S Chintamanani Z Chen L Zhu BN Kunkel 2004 Activation of a COI1-dependent pathway in Arabidopsis by Pseudomonas syringae type III effectors and coronatine Plant J 37 589 602 10.1111/j.1365-313X.2003.01986.x 1:CAS:528:DC%2BD2cXisVWhsbk%3D 14756769 (Pubitemid 38258779)