Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera

Scientia Horticulturae

Volumn 123, Issue 1, 2009, Pages 73-81

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

^a INSTITUTE OF EDIBLE FUNGI   (China)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

^c Max)   (United States)

^d ALBERTA RESEARCH COUNCIL   (Canada)

^e YANGZHOU UNIVERSITY   (China)

Author keywords

AP2 ERF; Gene duplication; In silico Mapping; Transcription factor; Vitis vinifera

Indexed keywords

AMINO ACID; CHEMICAL ANALYSIS; DECIDUOUS TREE; DICOTYLEDON; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; MONOCOTYLEDON; NUCLEIC ACID; PHYLOGENETICS; PHYSICAL ANALYSIS; RICE; STRESS RESISTANCE; VINE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; ORYZA SATIVA; POPULUS TRICHOCARPA; VITACEAE; VITIS; VITIS VINIFERA;

EID: 70349414286     PISSN: 03044238     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.scienta.2009.08.002     Document Type: Article

References (64)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., and Zhang Z. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
2. Bornhoff B.A., Harst M., Zyprian E., and Töpfer R. Transgenic plants of Vitis vinifera cv. Seyval blanc. Plant Cell Rep. 24 (2005) 433-438
3. Chen W.J., and Zhu T. Networks of transcription factors with roles in environmental stress response. Trends Plant Sci. 9 (2004) 591-596
4. Chenna R., Sugawara H., Koike T., Lopez R., and Gibson T.J. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31 (2003) 3497-3500
5. Dhekney S.A., Li Z.T., Dutt M., and Gray D.J. Agrobacterium-mediated transformation of embryogenic cultures and plant regeneration in Vitis rotundifolia Michx. (muscadine grape). Plant Cell Rep. 27 (2008) 865-872
6. Doligez A., Audiot E., Baumes R., and This P. QTLs for muscat flavor and monoterpenic odorant content in grapevine (Vitis vinifera L.). Mol. Breeding 18 (2006) 109-125
7. Dubouzet J.G., Sakuma Y., Ito Y., Kasuga M., and Dubouzet E.G. OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J. 33 (2003) 751-763
8. Dutt M., Li Z.T., Dhekney S.A., and Gray D.J. Transgenic plants from shoot apical meristems of Vitis vinifera L. "Thompson Seedless" via Agrobacterium-mediated transformation. Plant Cell Rep. 26 (2007) 2101-2110
9. Elliott R.C., Betzner A.S., Huttner E., Oakes M.P., and Tucker W.Q. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell 8 (1996) 155-168
10. Fowler S., and Thomashow M.F. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14 (2002) 1675-1690
11. Fu X.Y., Zhang Z., Peng R.H., Xiong A.S., and Liu J.G. Isolation and characterization of a novel cDNA encoding ERF/AP2-type transcription factor OsAP25 from Oryza sativa L. Biotechnol. Lett. 29 (2007) 1293-1299
12. Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., and Appel R.D. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31 (2003) 3784-3788
13. Gilmour S.J., Zarka D.G., Stockinger E.J., Salazar M.P., and Houghton J.M. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16 (1998) 433-442
14. Gilmour S.J., Sebolt A.M., Salazar M.P., Everard J.D., and Thomashow M.F. Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol. 124 (2000) 1854-1865
15. Goff S.A., Ricke D., Lan T.H., Presting G., and Wang R. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296 (2002) 92-100
16. Guo A., He K., Liu D., Bai S., and Gu X. DATF: a database of Arabidopsis transcription factors. Bioinformatics 21 (2005) 2568-2569
17. Gutterson N., and Reuber T.L. Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7 (2004) 465-471
18. He P., Chintamanani S., Chen Z., Zhu L., and Kunkel B.N. Activation of a COI1-dependent pathway in Arabidopsis by Pseudomonas syringae type III effectors and coronatine. Plant J. 37 (2004) 589-602
19. Iocco P., Franks T., and Thomas M.R. Genetic transformation of major wine grape cultivars of Vitis vinifera L. Transgenic Res. 10 (2001) 105-112
20. Irish V.F., and Sussex I.M. Function of the apetala-1 gene during Arabidopsis floral development. Plant Cell 2 (1990) 741-753
21. Ito Y., Katsura K., Maruyama K., Taji T., and Kobayashi M. Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol. 47 (2006) 141-153
22. Jaillon O., Aury J.M., Noel B., Policriti A., and Clepet C. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
23. Kellogg E.A. What happens to genes in duplicated genomes. Proc. Natl. Acad. Sci. USA 100 (2003) 4369-4371
24. Kikkert J.R., Striem M.J., Vidal J.R., and Wallace P.G. Long term study of somatic embryogenesis from anthers and ovaries of 12 grapevine (vitis sp.) Genotypes. In Vitro Cell Dev. Biol. Plant 41 (2005) 232-239
25. Kizis D., Lumbreras V., and Pagès M. Role of AP2/EREBP transcription factors in gene regulation during abiotic stress. FEBS Lett. 498 (2001) 187-189
26. Klucher K.M., Chow H., Reiser L., and Fischer R.L. The AINTEGUMENTA gene of Arabidopsis required for ovule and female gametophyte development is related to the floral homeotic gene APETALA2. Plant Cell 8 (1996) 137-153
27. Liu Q., Kasuga M., Sakuma Y., Abe H., and Miura S. 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 (1998) 1391-1406
28. Liu J.G., Zhang Z., Qin Q.L., Peng R.H., and Xiong A.S. Isolated and characterization of a cDNA encoding ethylene-responsive element binding protein (EREBP)/AP2-type protein, RCBF2, in Oryza sativa L. Biotechnol. Lett. 29 (2007) 165-173
29. Magnani E., Sjölander K., and Hake S. From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell 16 (2004) 2265-2277
30. Mezzetti B., Pandolfini T., Navacchi O., and Landi L. Genetic transformation of Vitis vinifera via organogenesis. BMC Biotechnol. 2 (2002) 18
31. Moore R.C., and Purugganan M.D. The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. USA 100 (2003) 15682-15687
32. Moore R.C., and Purugganan M.D. The evolutionary dynamics of plant duplicate genes. Curr. Opin. Plant Biol. 8 (2005) 122-128
33. Nakano T., Suzuki K., Fujimura T., and Shinshi H. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140 (2006) 411-432
34. Okamuro J.K., Caster B., Villarroel R., Van Montagu M., and Jofuku K.D. The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc. Natl. Acad. Sci. USA 94 (1997) 7076-7081
35. Riano P.D.M., Ruzicic S., Dreyer I., and Mueller R.B. PlnTFDB: An integrative plant transcription factor database. BMC Bioinform. 8 (2007) 42
36. Riechmann J.L., and Meyerowitz E.M. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379 (1998) 633-646
37. Riechmann J.L., Heard J., Martin G., Reuber L., and Jiang C. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290 (2000) 2105-2110
38. Qin Q.L., Liu J.G., Zhang Z., Peng R.H., and Xiong A.S. Isolation, optimization, and functional analysis of the cDNA encoding transcription factor RdreB1 in Oryza Sativa L. Mol. Breeding 19 (2007) 329-340
39. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
40. Sakuma Y., Liu Q., Dubouzet J.G., Abe H., and Shinozaki K. 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 (2002) 998-1009
41. Sémon M., and Wolfe K.H. Consequences of genome duplication. Curr. Opin. Genet. Dev. 17 (2007) 505-512
42. Shinwari Z.K., Nakashima K., Miura S., Kasuga M., and Seki M. An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression. Biochem. Biophys. Res. Commun. 250 (1998) 161-170
43. Sugino R.P., and Innan H. Selection for more of the same product as a force to enhance concerted evolution of duplicated genes. Trends Genet. 22 (2006) 642-644
44. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: molecular evolutionary genetics analysis MEGA software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
45. Taylor J.S., and Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38 (2004) 615-643
46. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 796-815
47. This P., Lacombe T., and Thomas M.R. Historical origins and genetic diversity of wine grapes. Trends Genet. 22 (2006) 511-519
48. Tuskan G.A., Difazio S., Jansson S., Bohlmann J., and Grigoriev I. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 (2006) 1596-1604
49. Velasco R., Zharkikh A., Troggio M., Cartwright D.A., and Cestaro A. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2 (2007) e1326
50. Vidal J.R., Kikkert J.R., Donzelli B.D., Wallace P.G., and Reisch B.I. Biolistic transformation of grapevine using minimal gene cassette technology. Plant Cell Rep. 25 (2006) 807-814
51. Vivier M.A., and Pretorius I.S. Genetically tailored grapevines for the wine industry. Trends Biotechnol. 20 (2002) 472-478
52. Wang W., Vinocur B., and Altman A. Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218 (2003) 1-14
53. Wang Q., Li P., Hanania U., Sahar N., Mawassi M., and Gafny R. Improvement of Agrobacterium-mediated transformation efficiency and transgenic plant regeneration of Vitis vinifera L. by optimizing selection regimes and tilizing cryopreserved cell suspensions. Plant Sci 168 (2005) 565-571
54. Wessler S.R. Homing into the origin of the AP2 DNA binding domain. Trends Plant Sci. 10 (2005) 54-56
55. Wilkinson D.L., and Harrison R.G. Predicting the solubility of recombinant proteins in Escherichia coli. BioTechnology 9 (1991) 443-448
56. Xiao H., Siddiqua M., Braybrook S., and Nassuth A. Three grape CBF/DREB1 genes respond to low temperature, drought and abscisic acid. Plant Cell Environ. 29 (2006) 1410-1421
57. Xiao H., Tattersall E.A., Siddiqua M.K., Cramer G.R., and Nassuth A. CBF4 is a unique member of the CBF transcription factor family of Vitis vinifera and Vitis riparia. Plant Cell Environ. 31 (2008) 1-10
58. Xiong A.S., Peng R.H., Zhuang J., Gao F., Zhu B., and Fu X.Y. Gene duplication and transfer events in plant mitochondria genome. Biochem. Biophys. Res. Commun. 376 (2008) 1-4
59. Xiong A.S., Peng R.H., Zhuang J., Gao F., Zhu B., and Fu X.Y. Gene duplication, transfer, and evolution in the chloroplast genome. Biotechnol. Adv. 27 (2009) 340-347
60. Yamaguchi S.K., and Shinozaki K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu. Rev. Plant. Biol. 57 (2006) 781-803
61. Yang T.W., Zhang L.J., Zhang T.G., Zhang H., and Xu S.J. Transcriptional regulation network of cold-responsive genes in higher plants. Plant Sci. 169 (2005) 987-995
62. Yang X., Tuskan G.A., and Cheng M.Z. Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiol. 142 (2006) 820-830
63. Yu J., Hu S., Wang J., Wong G.K., and Li S. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (2002) 79-92
64. Zhuang J., Cai B., Peng R.H., Zhu B., and Jin X.F. Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem. Biophys. Res. Commun. 371 (2008) 468-474