A genome-wide analysis of the ERF gene family in sorghum

Genetics and Molecular Research

Volumn 12, Issue 2, 2013, Pages 2038-2055

  Yan, H W ^a   Hong, L ^a   Zhou, Y Q ^a   Jiang, H Y ^a   Zhu, S W ^a   Fan, J ^a   Cheng, B J ^a  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

Author keywords

Expression; Genomic database; Phylogeny; SbERF

Indexed keywords

ARTICLE; BIOINFORMATICS; CHROMOSOME IDENTIFICATION; CONTROLLED STUDY; ETHYLENE RESPONSE FACTOR 1 GENE; ETHYLENE RESPONSE FACTOR 105 GENE; ETHYLENE RESPONSE FACTOR 14 GENE; ETHYLENE RESPONSE FACTOR 19 GENE; ETHYLENE RESPONSE FACTOR 20 GENE; ETHYLENE RESPONSE FACTOR 26 GENE; ETHYLENE RESPONSE FACTOR 5 GENE; ETHYLENE RESPONSE FACTOR 57 GENE; ETHYLENE RESPONSE FACTOR 7 GENE; ETHYLENE RESPONSE FACTOR 71 GENE; ETHYLENE RESPONSE FACTOR 72 GENE; ETHYLENE RESPONSE FACTOR 74 GENE; ETHYLENE RESPONSE FACTOR GENE; GENE; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE MAPPING; GENE STRUCTURE; GENETIC ASSOCIATION; MAIZE; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; NONHUMAN; PLANT GENE; SEQUENCE ANALYSIS; SORGHUM; SPECIES DIFFERENCE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ARABIDOPSIS; CHROMOSOMES, PLANT; CONSERVED SEQUENCE; ETHYLENES; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME-WIDE ASSOCIATION STUDY; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; PROTEIN STRUCTURE, TERTIARY; SORGHUM; TRANSCRIPTION FACTORS; ZEA MAYS;

ARABIDOPSIS; VITACEAE; ZEA MAYS;

EID: 84879290681     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: 10.4238/2013.May.13.1     Document Type: Article

References (41)

1. Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, et al. (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: 5484-5496.
2. Alonso JM, Stepanova AN, Solano R, Wisman E, et al. (2003). Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 100: 2992-2997.
3. Bailey TL, Williams N, Misleh C and Li WW (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.
4. Baker SS, Wilhelm KS and Thomashow MF (1994). The 5-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought-and ABA-regulated gene expression. Plant Mol. Biol. 24: 701-713.
5. Banno H, Ikeda Y, Niu QW and Chua NH (2001). Overexpression of Arabidopsis ESR1 induces initiation of shoot regeneration. Plant Cell 13: 2609-2618.
6. Berrocal-Lobo M, Molina A and Solano R (2002). Constitutive expression of ETHYLENE-RESPONSE-FACTOR1 in Arabidopsis confers resistance to several necrotrophic fungi. Plant J. 29: 23-32.
7. Boutilier K, Offringa R, Sharma VK, Kieft H, et al. (2002). Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell 14: 1737-1749.
8. Buttner M and Singh KB (1997). Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein. Proc. Natl. Acad. Sci. U. S. A. 94: 5961-5966.
9. Caetano-Anollés G (2001). Novel strategies to study the role of mutation and nucleic acid structure in evolution. Plant Cell Tiss. Org. 67: 115-132.
10. Chuck G, Meeley RB and Hake S (1998). The control of maize spikelet meristem fate by the APETALA2-like gene indeterminate spikelet1. Genes Dev. 12: 1145-1154.
11. Chuck G, Muszynski M, Kellogg E, Hake S, et al. (2002). The control of spikelet meristem identity by the branched silkless1 gene in maize. Science 298: 1238-1241.
12. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, et al. (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.
13. Elliott RC, Betzner AS, Huttner E, Oakes MP, et al. (1996). AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell 8: 155-168.
14. Engel W, Hof JO and Wolf U (1970). Gene duplication by polyploid evolution: the isoenzyme of the sorbitol dehydrogenase in herring-and salmon-like fishes (Isospondyli). Humangenetik 9: 157-163.
15. Gu YQ, Wildermuth MC, Chakravarthy S, Loh YT, et al. (2002). Tomato transcription factors pti4, pti5, and pti6 activate defense responses when expressed in Arabidopsis. Plant Cell 14: 817-831.
16. Gutterson N and Reuber TL (2004). Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7: 465-471.
17. Hao D, Yamasaki K, Sarai A and Ohme-Takagi M (2002). Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry 41: 4202-4208.
18. Hu X, Cheng X, Jiang H, Zhu S, et al. (2010). Genome-wide analysis of cyclins in maize (Zea mays). Genet. Mol. Res. 9: 1490-1503.
19. Hu YX, Wang YX, Liu XF and Li JY (2004). Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res. 14: 8-15.
20. Jin LG and Liu JY (2008). Molecular cloning, expression profile and promoter analysis of a novel ethylene responsive transcription factor gene GhERF4 from cotton (Gossypium hirstum). Plant Physiol. Biochem. 46: 46-53.
21. Kagaya Y, Ohmiya K and Hattori T (1999). RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 27: 470-478.
22. Moose SP and Sisco PH (1996). Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity. Genes Dev. 10: 3018-3027.
23. Nakano T, Suzuki K, Fujimura T and Shinshi H (2006). Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140: 411-432.
24. Ohta M, Matsui K, Hiratsu K, Shinshi H, et al. (2001). Repression domains of class II ERF transcriptional repressors share an essential motif for active repression. Plant Cell 13: 1959-1968.
25. Okamuro JK, Caster B, Villarroel R, Van MM, et al. (1997). The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 94: 7076-7081.
26. Riechmann JL and Meyerowitz EM (1998). The AP2/EREBP family of plant transcription factors. Biol. Chem. 379: 633-646.
27. Sakuma Y, Liu Q, Dubouzet JG, Abe H, et al. (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.
28. Shin R, Park JM, An JM and Paek KH (2002). Ectopic expression of Tsi1 in transgenic hot pepper plants enhances host resistance to viral, bacterial, and oomycete pathogens. Mol. Plant Microbe Interact. 15: 983-989.
29. Shinshi H, Usami S and Ohme-Takagi M (1995). Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene. Plant. Mol. Biol. 27: 923-932.
30. Stockinger EJ, Gilmour SJ and Thomashow MF (1997). Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl. Acad. Sci. U. S. A. 94: 1035-1040.
31. Stolf-Moreira R, Medri ME, Neumaier N, Lemos NG, et al. (2010). Cloning and quantitative expression analysis of drought-induced genes in soybean. Genet. Mol. Res. 9: 858-867.
32. Sun S, Yu JP, Chen F, Zhao TJ, et al. (2008). TINY, a dehydration-responsive element (DRE)-binding protein-like transcription factor connecting the DRE-and ethylene-responsive element-mediated signaling pathways in Arabidopsis. J. Biol. Chem. 283: 6261-6271.
33. Tamura K, Dudley J, Nei M and Kumar S (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
34. Thomashow MF (1999). PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 571-599.
35. Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
36. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, et al. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
37. van der Graaff E, Dulk-Ras AD, Hooykaas PJ and Keller B (2000). Activation tagging of the LEAFY PETIOLE gene affects leaf petiole development in Arabidopsis thaliana. Development 127: 4971-4980.
38. Wang QJ, Xu KY, Tong ZG, Wang SH, et al. (2010). Characterization of a new dehydration responsive element binding factor in central arctic cowberry. Plant Cell Tiss. Org. 101: 211-219.
39. Yamaguchi-Shinozaki K and Shinozaki K (1994). A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6: 251-264.
40. Zhang G, Chen M, Chen X, Xu Z, et al. (2008). Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.). J. Exp. Bot. 59: 4095-4107.
41. Zhuang J, Cai B, Peng RH, Zhu B, et al. (2008). Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem. Biophys. Res. Commun. 371: 468-474.