Abstract
The basic leucine zipper (bZIP) transcription factors comprise a family of transcriptional regulators present extensively in plants, involved in regulating diverse biological processes such as flower and vascular development, seed maturation, stress signaling and pathogen defense. Castor bean (Ricinus communis L. Euphorbiaceae) is one of the most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. We performed a comprehensive genome-wide identification and analysis of the bZIP transcription factors that exist in the castor bean genome in this study. In total, 49 RcbZIP transcription factors were identified, characterized and categorized into 11 groups (I–XI) based on their gene structure, DNA-binding sites, conserved motifs, and phylogenetic relationships. The dimerization properties of 49 RcbZIP proteins were predicted on the basis of the characteristic features in the leucine zipper. Global expression profiles of 49 RcbZIP genes among different tissues were examined using high-throughput sequencing of digital gene expression profiles, and resulted in diverse expression patterns that may provide basic information to further reveal the function of the 49 RcbZIP genes in castor bean. The results obtained from this study would provide valuable information in understanding the molecular basis of the RcbZIP transcription factor family and their potential function in regulating the growth and development, particularly in seed filling of castor bean.
Similar content being viewed by others
Abbreviations
- Leu:
-
Leucine
- Asn:
-
Asparagines
- bZIP:
-
Basic leucine zipper
- DGE:
-
Digital gene expression profiling
References
Acharya A, Ruvinov SB, Gal J, Moll JR, Vinson C (2002) A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K. Biochemistry 41:14122–14131
Aeschbacher RA, Schrott M, Potrykus I, Saul MW (1991) Isolation and molecular characterization of PosF21, an Arabidopsis thaliana gene which shows characteristics of a b-Zip class transcription factor. Plant J 1:303–316
Akpan U, Jimoh A, Mohammed A (2006) Extraction, characterization and modification of castor seed oil. Leonardo J Sci 8:43–52
Bensmihen S, Giraudat J, Parcy F (2005) Characterization of three homologous basic leucine zipper transcription factors (bZIP) of the ABI5 family during Arabidopsis thaliana embryo maturation. J Exp Bot 56:597–603
Betts MJ, Guigo R, Agarwal P, Russell RB (2001) Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution? EMBO J 20:5354–5360
Brown BA, Jenkins GI (2008) UV-B signaling pathways with different fluence-rate response profiles are distinguished in mature Arabidopsis leaf tissue by requirement for UVR8, HY5, and HYH. Plant Physiol 146:576–588
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 (2010) Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 28:951–953
Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N (1998) Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10:673–683
Choi HI, Hong JH, Ha JO, Kang JY, Kim SY (2000) ABFs, a family of ABA-responsive element binding factors. J Biol Chem 275:1723–1730
Deppmann CD, Acharya A, Rishi V, Wobbes B, Smeekens S, Taparowsky EJ, Vinson C (2004) Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs. Nucleic Acids Res 32:3435–3445
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Ellenberger TE, Brandl CJ, Struhl K, Harrison SC (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha-helices: crystal structure of the protein-DNA complex. Cell 71:1223–1237
Emili A, Greenblatt J, Ingles CJ (1994) Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein. Mol Cell Biol 14:1582–1593
Finkelstein RR, Lynch TJ (2000) The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell 12:599–609
Foster R, Izawa T, Chua NH (1994) Plant bzip proteins gather at ACGT elements. FASEB J 8:192–200
Hobo T, Kowyama Y, Hattori T (1999) A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription. P Natl Acad Sci USA 96:15348–15353
Hodges RS, Sodek J, Smillie LB, Jurasek L (1973) Tropomyosin: amino acid sequence and coiled-coil structure. Cold Spring Harb Sym 37:299–310
Holm M, Ma LG, Qu LJ, Deng XW (2002) Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Gene Dev 16:1247–1259
Hossain MA, Cho JI, Han M, Ahn CH, Jeon JS, An G, Park PB (2010a) The ABRE-binding bZIP transcription factor OsABF2 is a positive regulator of abiotic stress and ABA signaling in rice. J Plant Physiol 167:1512–1520
Hossain MA, Lee Y, Cho JI, Ahn CH, Lee SK, Jeon JS, Kang H, Lee CH, An G, Park PB (2010b) The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signaling in rice. Plant Mol Biol 72:557–566
Hurst HC (1995) Transcription factors.1. Bzip proteins. Protein Profile 2:105–168
Izawa T, Foster R, Chua NH (1993) Plant bZIP protein DNA binding specificity. J Mol Biol 230:1131–1144
Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F, ZIPRG b (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7:106–111
Kang JY, Choi HI, Im MY, Kim SY (2002) Arabidopsis basic leucine zipper proteins that mediate stress-responsive abscisic acid signaling. Plant Cell 14:343–357
Katagiri F, Lam E, Chua NH (1989) Two tobacco DNA-binding proteins with homology to the nuclear factor CREB. Nature 340:727–730
Landschulz WH, Johnson PF, Mcknight SL (1988) The leucine zipper: a hypothetical structure common to a new class of DNA-binding proteins. Science 240:1759–1764
Li RQ, Yu C, Li YR, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967
Liao Y, Zou HF, Wei W, Hao YJ, Tian AG, Huang J, Liu YF, Zhang JS, Chen SY (2008) Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis. Planta 228:225–240
Lu G, Gao CX, Zheng XN, Han B (2009) Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 229:605–615
Meier I, Gruissem W (1994) Novel conserved sequence motifs in plant G-box binding-proteins and implications for interactive domains. Nucleic Acids Res 22:470–478
Moitra J, Szilak L, Krylov D, Vinson C (1997) Leucine is the most stabilizing aliphatic amino acid in the d position of a dimeric leucine zipper coiled coil. Biochemistry 36:12567–12573
Nakagawa H, Ohmiya K, Hattori T (1996) A rice bZIP protein, designated OSBZ8, is rapidly induced by abscisic acid. Plant J 9:217–227
Nakase M, Aoki N, Matsuda T, Adachi T (1997) Characterization of a novel rice bZIP protein which binds to the alpha-globulin promoter. Plant Mol Biol 33:513–522
Nijhawan A, Jain M, Tyagi AK, Khurana JP (2008) Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol 146:333–350
Niu XP, Renshaw-Gegg L, Miller L, Guiltinan MJ (1999) Bipartite determinants of DNA-binding specificity of plant basic leucine zipper proteins. Plant Mol Biol 41:1–13
Ogunniyi DS (2006) Castor oil: a vital industrial raw material. Bioresource Technol 97:1086–1091
Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, Kim YK, Nahm BH, Kim JK (2005) Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol 138:341–351
Oshea EK, Rutkowski R, Kim PS (1992) Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68:699–708
Pinna LA (1990) Casein kinase 2: an ‘eminence grise’ in cellular regulation? Biochim Biophys Acta 1054:267–284
Qiu L, Yang C, Tian B, Yang JB, Liu A (2010) Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 10:278
Qu GZ, Zang LN, Hu XL, Gao CQ, Zheng TC, Li KL (2012) Co-transfer of LEA and bZip genes from Tamarix confers additive salt and osmotic stress tolerance in transgenic tobacco. Plant Mol Biol Rep 30:512–518
Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu CL (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110
Rook F, Gerrits N, Kortstee A, van Kampen M, Borrias M, Weisbeek P, Smeekens S (1998) Sucrose-specific signalling represses translation of the Arabidopsis ATB2 bZIP transcription factor gene. Plant J 15:253–263
Scheffzek K, Grunewald P, Wohlgemuth S, Kabsch W, Tu H, Wigler M, Wittinghofer A, Herrmann C (2001) The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast. Structure 9:1043–1050
Schindler U, Menkens AE, Beckmann H, Ecker JR, Cashmore AR (1992) Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF Bzip proteins. EMBO J 11:1261–1273
Scholza V, da Silva JN (2008) Prospects and risks of the use of castor oil as a fuel. Biomass Bioenerg 32:95–100
Schworer CM, Colbran RJ, Keefer JR, Soderling TR (1988) Ca2+/calmodulin-dependent protein kinase II. Identification of a regulatory autophosphorylation site adjacent to the inhibitory and calmodulin-binding domains. J Biol Chem 263:13486–13489
Shen HS, Cao KM, Wang XP (2007) A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer. Biochem Biophys Res Comm 362:425–430
Shimizu H, Sato K, Berberich T, Miyazaki A, Ozaki R, Imai R, Kusano T (2005) LIP19, a basic region leucine zipper protein, is a fos-like molecular switch in the cold signaling of rice plants. Plant Cell Physiol 46:1623–1634
Suckow M, von Wilcken-Bergmann B, Müller-Hill B (1993) Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding. EMBO J 12:1193–1200
Tak H, Mhatre M (2013) Cloning and molecular characterization of a putative bZIP transcription factor VvbZIP23 from Vitis vinifera. Protoplasma 250:333–345
Talanian RV, Mcknight CJ, Kim PS (1990) Sequence-specific DNA-binding by a short peptide dimer. Science 249:769–771
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 28:2731–2739
Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, Yamaguchi-Shinozaki K (2000) Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. P Natl Acad Sci USA 97:11632–11637
Vinson CR, Hai TW, Boyd SM (1993) Dimerization specificity of the leucine zipper-containing bzip motif on DNA binding: prediction and rational design. Gene Dev 7:1047–1058
Wang JZ, Zhou JX, Zhang BL, Vanitha J, Ramachandran S, Jiang SY (2011) Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum. J Integr Plant Biol 53:212–231
Wei KF, Chen J, Wang YM, Chen YH, Chen SX, Lin YN, Pan S, Zhong XJ, Xie DX (2012) Genome-wide analysis of bZIP-encoding genes in maize. DNA Res 19:463–476
Yin YH, Zhu Q, Dai SH, Lamb C, Beachy RN (1997) RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development. EMBO J 16:5247–5259
Zeng X, Herndon AM, Hu JC (1997) Buried asparagines determine the dimerization specificities of leucine zipper mutants. P Natl Acad Sci USA 94:3673–3678
Zou MJ, Guan YC, Ren HB, Zhang F, Chen F (2008) A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance. Plant Mol Biol 66:675–683
Acknowledgments
We thank Zibo Academy of Agricultural Sciences, Shandong, China for providing the seeds of castor bean var. ZB306 elite inbred line. This work was supported by the “Hundreds of Talents” program of the Chinese Academy of Sciences (AL).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Jin, Z., Xu, W. & Liu, A. Genomic surveys and expression analysis of bZIP gene family in castor bean (Ricinus communis L.). Planta 239, 299–312 (2014). https://doi.org/10.1007/s00425-013-1979-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00425-013-1979-9