Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.)

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Xu, Wei ^a,b   Li, Fei ^a   Ling, Lizhen ^a   Liu, Aizhong ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AP2 PROTEIN; ERF PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; TRANSCRIPTION FACTOR AP 2; TRANSCRIPTOME; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; AP2 GENE; ARTICLE; CONTROLLED STUDY; ERF GENE; GENE EXPRESSION PROFILING; GENE STRUCTURE; GENETIC ASSOCIATION; HIGH THROUGHPUT SEQUENCING; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PLANT GENE; PLANT GENOME; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; RICINUS COMMUNIS; BIOSYNTHESIS; CLASSIFICATION; GENE EXPRESSION REGULATION; GENETICS;

RICINUS COMMUNIS;

AMINO ACID SEQUENCE; CASTOR BEAN; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MULTIGENE FAMILY; PHYLOGENY; PLANT PROTEINS; TRANSCRIPTION FACTOR AP-2; TRANSCRIPTOME;

EID: 84887379265     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-785     Document Type: Article

References (60)

1. Riechmann JL, Meyerowitz EM. The AP2/EREBP family of plant transcription factors. Biol Chem 1998, 379:633-646.
2. Wessler SR. Homing into the origin of the AP2 DNA binding domain. Trends in Plant Sci 2005, 10:54-56.
3. Jofuku KD, den Boer BGW, van Montagu M, Okamuro JK. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 1994, 6:1211-1225.
4. Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQJ, Gerentes D, Perez P, Smyth DR. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell 1996, 8:155-168.
5. Shigyo M, Ito M. Analysis of gymnosperm two-AP2-domain-containing genes. Dev Genes Evol 2004, 214(3):105-14.
6. Aukerman MJ, Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 2003, 15:2730-2741.
7. Jofuku KD, Omidyar PK, Gee Z, Okamuro JK. Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc Natl Acad Sci U S A 2005, 102:3117-3122.
8. Nole-Wilson S, Krizek BA. DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. Nucleic Acids Res 2000, 21:4076-4082.
9. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Yamaguchi-Shinozaki K. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochemical d Biophyisical Res Comm 2002, 290:998-1009.
10. Ohme-Takagi M, Shinshi H. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 1995, 7:173-182.
11. Hao DY, Ohme-Takagi M, Sarai A. Unique mode of GCC box recognition by the DNA-binding domain of ethylene responsive element-binding factor (ERF domain) in plants. J Biol Chem 1998, 273:26857-26861.
12. Yamaguchi-Shinozaki K, Shinozaki K. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 1994, 6:251-264.
13. Jiang C, Iu B, Singh J. Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol Biol 1996, 30:679-684.
14. Giraudat J, Hauge BM, Valon C, Smalle J, Parcy F, Goodman HM. Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell 1992, 4:1251-1261.
15. Suzuki M, Kao CY, McCarty DR. The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell 1997, 9:799-807.
16. Kagaya Y, Ohmiya K, Hattori T. 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 1999, 27:470-478.
17. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 2003, 30:653-657.
18. Hu YX, Wang YX, Liu XF, Li JY. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res 2004, 14:8-15.
19. Sohn KH, Lee SC, Jung HW, Hong JK, Hwang BK. Expression and functional roles of the pepper pathogen-induced transcription factor RAV1 in bacterial disease resistance, and drought and salt stress tolerance. Plant Mol Biol 2006, 61:897-915.
20. Li CW, Su RC, Cheng CP, Sanjay, You SJ, Hsieh TH, Chao TC, Chan MT. Tomato RAV transcription factor is a pivotal modulator involved in the AP2/EREBP-mediated defense pathway. Plant Physiol 2011, 156:213-227.
21. Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, Xue Y, Gao F, Fu XY, Tian YS, Zhao W, Qiao YS, Zhang Z, Xiong AS, Yao QH. Genome-wide analysis of the AP2/ERF gene family in populus trichocarpa. Biochem Biophys Res Commun 2008, 371:468-474.
22. Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M, Perata P. Genomic and transcriptomic analysis of the AP2/ERF superfamily in vitis vinifera. BMC Genomics 2010, 11:719.
23. Rashid M, Guangyuan H, Guangxiao Y, Hussain J, Xu Y. AP2/ERF transcription factor in rice: genome-wide canvas and syntenic relationships between monocots and eudicots. Evol Bioinform Online 2012, 8:321-355.
24. Zhuang J, Chen JM, Yao QH, Xiong F, Sun CC, Zhou XR, Zhang J, Xiong AS. Discovery and expression profile analysis of AP2/ERF family genes from Triticum aestivum. Mol Biol Rep 2011, 38:745-753.
25. Zhang CH, Shangguan LF, Ma RJ, Sun X, Tao R, Guo L, Korir NK, Yu ML. Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica). Genet Mol Res 2012, 11:4789-4809.
26. Akpan U, Jimoh A. Mohammed AExtraction: characterization and modification of castor seed oil. Leonardo J Sci 2006, 8:43-52.
27. Ogunniyi DS. Castor oil: a vital industrial raw material. Bioresour Technol 2006, 97:1086-1091.
28. Scholz V, da Silva JN. Prospects and risks of the use of castor oil as a fuel. Biomass Bioenergy 2008, 32:95-100.
29. Qiu L, Yang C, Tian B, Yang JB, Liu A. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 2010, 10:278.
30. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicz PD. Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 2010, 28:951-956.
31. Nakano T, Suzuki K, Fujimura T, Shinshi H. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 2006, 140:411-432.
32. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
33. Wei X, Cui QH, Li F, Liu AZ. Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.). PLoS ONE 2013, 8:e69995.
34. Brown AP, Kroon JTM, Swarbreck D, Febrer M, Larson TR, Graham IA, Caccamo M, Slabas AR. Tissue-specific whole transcriptome sequencing in Castor, directed at understanding triacylglycerol lipid biosynthetic pathways. PLoS ONE 2012, 7:e30100.
35. Magnani E, Sjölander K, Hake S. From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell 2004, 16:2265-2277.
36. Okamuro JK, Caster B, Villarroel R, Van Montagu M, Jofuku KD. The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc Natl Acad Sci U S A 1997, 94:7076-7081.
37. Kim S, Soltis PS, Wall K, Soltis DE. Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol 2006, 23:107-120.
38. Albrecht V, Ritz O, Linder S, Harter K, Kudla J. The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases. EMBO J 2001, 20:1051-1063.
39. Qu LJ, Zhu YX. Transcription factor families in Arabidopsis: major progress and outstanding issues for future research. Curr Opin Plant Biol 2006, 9:544-549.
40. Feng JX, Liu D, Pan Y, Gong W, Ma LG, Luo JC, Deng XW, Zhu YX. An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family. Plant Mol Biol 2005, 59:853-868.
41. Hagen G, Guilfoyle T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol 2002, 49:373-385.
42. Manosalva PM, Davidson RM, Liu B, Zhu X, Hulbert SH, Leung H, Leach JE. A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiol 2009, 149:286-296.
43. Tiwari SB, Belachew A, Ma SF, Young M, Ade J, Shen Y, Marion CM, Holtan HE, Bailey A, Stone JK, Edwards L, Wallace AD, Canales RD, Adam L, Ratcliffe OJ, Repetti PP. The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors. Plant J 2012, 70:855-865.
44. Wollmann H, Mica E, Todesco M, Long JA, Weigel D. On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development. Development 2010, 137:3633-3642.
45. Hong LZ, Li J, Schmidt-Küntzel A, Warren WC, Barsh GS. Digital gene expression for non-model organisms. Genome Res 2011, 21:1905-1915.
46. Galinha C, Hofhuis H, Luijten M, Willemsen V, Blilou I, Heidstra R, Scheres B. PLETHORA proteins as dose-dependent master regulators of Arabidopsis root development. Nature 2007, 449:1053-1057.
47. Licausi F, van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P. HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J 2010, 62:302-315.
48. Licausi F, Weits DA, Pant BD, Scheible WR, Geigenberger P, van Dongen JT. Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability. New Phytol 2011, 190:442-456.
49. Hess N, Klode M, Anders M, Sauter M. The hypoxia responsive transcription factor genes ERF71/HRE2 and ERF73/HRE1 of Arabidopsis are differentially regulated by ethylene. Physiol Plant 2011, 143:41-49.
50. Yang CY, Hsu FC, Li JP, Wang NN, Shih MC. The AP2/ERF transcription factor AtERF73/HRE1 modulates ethylene responses during hypoxia in Arabidopsis. Plant Physiol 2011, 156:202-212.
51. Cernac A, Benning C. WRINKLED1 Encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J 2004, 40:575-585.
52. Baud S, Wuillème S, To A, Rochat C, Lepiniec L. Role of WRINKLED1 in the transcriptional regulation of glycolytic and fatty acid biosynthetic genes in Arabidopsis. Plant J 2009, 60:933-947.
53. Maeo K, Tokuda T, Ayame A, Mitsui N, Kawai T, Tsukagoshi H, Ishiguro S, Nakamura K. An AP2-type transcription factor, WRINKLED1, of Arabidopsis thaliana binds to the AW-box sequence conserved among proximal upstream regions of genes involved in fatty acid synthesis. Plant J 2009, 60:476-487.
54. Liu J, Hua W, Zhan G, Wei F, Wang X, Liu G, Wang H. Increasing seed mass and oil content in transgenic Arabidopsis by the overexpression of wri1-like gene from Brassica napus. Plant Physiol Biochem 2010, 48:9-15.
55. Pouvreau B, Baud S, Vernoud V, Morin V, Py C, Gendrot G, Pichon JP, Rouster J, Paul W, Rogowsky PM. Duplicate maize Wrinkled1 transcription factors activate target genes involved in seed oil biosynthesis. Plant Physiol 2011, 156:674-686.
56. To A, Joubès J, Barthole G, Lécureuil A, Scagnelli A, Jasinski S, Lepiniec L, Baud S. WRINKLED transcription factors orchestrate tissue-specific regulation of fatty acid biosynthesis in Arabidopsis. Plant Cell 2012, 24:5007-5023.
57. 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. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23:2947-1948.
58. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
59. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25:1966-1967.
60. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80.