Genome-Wide Analysis of the AP2/ERF Gene Family in Prunus mume

Plant Molecular Biology Reporter

Volumn 31, Issue 3, 2013, Pages 741-750

  Du, Dongliang ^a   Hao, Ruijie ^a   Cheng, Tangren ^a   Pan, Huitang ^a   Yang, Weiru ^a   Wang, Jia ^a   Zhang, Qixiang ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

AP2 ERF; Chinese plum (Prunus mume); Transcription factor; Transcriptome sequencing analysis

Indexed keywords

ARABIDOPSIS; PRUNUS; PRUNUS DOMESTICA; PRUNUS MUME; ROSACEAE;

EID: 84877796551     PISSN: 07359640     EISSN: 15729818     Source Type: Journal    
DOI: 10.1007/s11105-012-0531-6     Document Type: Article

References (39)

1. Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M (1998) A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J 17(18): 5484-5496. doi: 10. 1093/emboj/17. 18. 5484.
2. Altenhoff AM, Dessimoz C (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 5(1). doi: 10. 1371/journal. pcbi. 1000262.
3. Cao ZF, Li J, Chen F, Li YQ, Zhou HM, Liu Q (2001) Effect of two conserved amino acid residues on DREB1A function. Biochem Mosc 66(6): 623-627. doi: 10. 1023/a: 1010251129429.
4. Chen N, Yang Q, Su M, Pan L, Chi X, Chen M, He Y, Yang Z, Wang T, Wang M, Yu S (2012) Cloning of Six ERF family transcription factor genes from peanut and analysis of their expression during abiotic stress. Plant Mol Biol Report 1-11.
5. Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, Perez P, Smyth DR (1996) AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell 8(2): 155-168. doi: 10. 1105/tpc. 8. 2. 155.
6. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-D222. doi: 10. 1093/nar/gkp985.
7. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-W37. doi: 10. 1093/nar/gkr367.
8. Guo A-Y, Zhu Q-H, Chen X, Luo J-C (2007) GSDS: a gene structure display server. Yi Chuan 29(8): 1023-1026.
9. Jofuku KD, den Boer BG, van Montagu M, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6(9): 1211-1225. doi: 10. 2307/3869820.
10. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36: D1034-D1040. doi: 10. 1093/nar/gkm803.
11. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2. 0. Bioinformatics 23(21): 2947-2948. doi: 10. 1093/bioinformatics/btm404.
12. Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M, Perata P (2010) Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genomics 11. doi: 10. 1186/1471-2164-11-719.
13. Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10(8): 1391-1406. doi: 10. 2307/3870648.
14. Liu L, Cao X-L, Bai R, Yao N, Li L-B, He C-F (2012) Isolation and characterization of the cold-induced Phyllostachys edulis AP2/ERF family transcription factor, peDREB1. Plant Mol Biol Rep 30(3): 679-689. doi: 10. 1007/s11105-011-0380-8.
15. Maes T, van de Steene N, Zethof J, Karimi M, D'Hauw M, Mares G, van Montagu M, Gerats T (2001) Petunia Ap2-like genes and their role in flower and seed development. Plant Cell 13(2): 229-244. doi: 10. 2307/3871273.
16. Maher C, Stein L, Ware D (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res 16(4): 510-519. doi: 10. 1101/gr. 4680506.
17. McDowall J, Hunter S (2011) InterPro protein classification. Methods Mol Biol (Clifton, NJ) 694: 37-47.
18. Meng X, Li F, Liu C, Zhang C, Wu Z, Chen Y (2010) Isolation and characterization of an ERF transcription factor gene from cotton (Gossypium barbadense L.). Plant Mol Biol Rep 28(1): 176-183.
19. Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2011) AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta-Gene Regul Mech 1819(2): 86-96. doi: 10. 1016/j. bbagrm. 2011. 08. 004.
20. Moose SP, Sisco PH (1996) Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity. Genes Dev 10(23): 3018-3027. doi: 10. 1101/gad. 10. 23. 3018.
21. Nakano T, Tsujimoto Y, Naito Y, Suzuki K, Fujimura T, Shinshi H (2004) Genome-wide analysis of the Arabidopsis and rice ERF gene families. Plant Cell Physiol 45: S204-S204.
22. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140(2): 411-432. doi: 10. 1104/pp. 105. 073783.
23. Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7(2): 173-182. doi: 10. 2307/3869993.
24. Riechmann JL, Meyerowitz EM (1998) The AP2/EREBP family of plant transcription factors. Biol Chem 379(6): 633-646.
25. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Yamaguchi-Shinozaki K (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(3): 998-1009. doi: 10. 1006/bbrc. 2001. 6299.
26. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37(5): 501-506.
27. Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi I-R, Omura T, Kikuchi S (2011) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol 52(2): 344-360. doi: 10. 1093/pcp/pcq196.
28. Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arus P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE (2008) Multiple models for Rosaceae genomics. Plant Physiol 147(3): 985-1003. doi: 10. 1104/pp. 107. 115618.
29. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton J-M, Rees DJG, Williams KP, Holt SH, Rojas JJR, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman T-L, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Girona EL, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM (2010) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43(2): 109-U151. doi: 10. 1038/ng. 740.
30. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36: D1009-D1014. doi: 10. 1093/nar/gkm965.
31. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731-2739. doi: 10. 1093/molbev/msr121.
32. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320(5875): 486-488. doi: 10. 1126/science. 1153917.
33. Tsaftaris AS, Pasentsis K, Madesis P, Argiriou A (2012) Sequence characterization and expression analysis of three APETALA2-like genes from Saffron crocus. Plant Mol Biol Rep 30(2): 443-452. doi: 10. 1007/s11105-011-0355-9.
34. van der Heijden RTJM, Snel B, van Noort V, Huynen MA (2007) Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinforma 8. doi: 10. 1186/1471-2105-8-83.
35. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel C-E, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42(10): 833-839. doi: 10. 1038/ng. 654.
36. Zarei A, Korbes AP, Younessi P, Montiel G, Champion A, Memelink J (2011) Two GCC boxes and AP2/ERF-domain transcription factor ORA59 in jasmonate/ethylene-mediated activation of the PDF1. 2 promoter in Arabidopsis. Plant Mol Biol 75(4-5): 321-331. doi: 10. 1007/s11103-010-9728-y.
37. Zhuang J, Cai B, Peng R-H, Zhu B, Jin X-F, Xue Y, Gao F, Fu X-Y, Tian Y-S, Zhao W, Qiao Y-S, Zhang Z, Xiong A-S, Yao Q-H (2008) Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem Biophys Res Commun 371(3): 468-474. doi: 10. 1016/j. bbrc. 2008. 04. 087.
38. Zhuang J, Peng R-H, Cheng Z-M, Zhang J, Cai B, Zhang Z, Gao F, Zhu B, Fu X-Y, Jin X-F, Chen J-M, Qiao Y-S, Xiong A-S, Yao Q-H (2009) Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera. Sci Hortic 123(1): 73-81. doi: 10. 1016/j. scienta. 2009. 08. 002.
39. Zhuang J, Yao Q-H, Xiong A-S, Zhang J (2011) Isolation, phylogeny and expression patterns of AP2-like genes in apple (Malus x domestica Borkh). Plant Mol Biol Rep 29(1): 209-216. doi: 10. 1007/s11105-010-0227-8.