Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice

Plant Physiology

Volumn 146, Issue 2, 2008, Pages 333-350

  Nijhawan, Aashima ^a   Jain, Mukesh ^a   Tyagi, Akhilesh K ^a   Khurana, Jitendra P ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; ORYZA SATIVA;

EID: 38949124519     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.107.112821     Document Type: Article

References (77)

1. Abe M, Kobayashi Y, Yamamoto S, Daimon Y, Yamaguchi A, Ikeda Y, Ichinoki H, Notaguchi M, Goto K, Araki T (2005) FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 309: 1052-1056
2. 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
3. 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
4. Aguan K, Sugawara K, Suzuki N, Kusano T (1993) Low-temperature-dependent expression of a rice gene encoding a protein with a leucine-zipper motif. Mol Gen Genet 240: 1-8
5. Bensmihen S, Rippa S, Lambert G, Jublot D, Pautot V, Granier F, Giraudat J, Parcy F (2002) The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis. Plant Cell 14: 1391-1403
6. Busk PK, Pages M (1998) Regulation of abscisic acid-induced transcription. Plant Mol Biol 37: 425-435
7. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4: 10
8. Cheong YH, Yoo CM, Park JM, Ryu GR, Goekjian VH, Nagao RT, Key JL, Cho MJ, Hong JC (1998) STF1 is a novel TGACG-binding factor with a zinc-finger motif and a bZIP domain which heterodimerizes with GBF proteins. Plant J 15: 199-209
9. Chern MS, Eiben HG, Bustos MM (1996) The developmentally regulated bZIP factor ROM1 modulates transcription from lectin and storage protein genes in bean embryos. Plant J 10: 135-148
10. Chuang CF, Running MP, Williams RW, Meyerowitz EM (1999) The PERIANTHIA gene encodes a bZIP protein involved in the determination of floral organ number in Arabidopsis thaliana. Genes Dev 13: 334-344
11. Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, Guimil S, Dunn M, Luginbuhl P, Ellero C, et al (2003) A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci USA 100: 4945-4950
12. Dai S, Petruccelli S, Ordiz MI, Zhang Z, Chen S, Beachy RN (2003) Functional analysis of RF2a, a rice transcription factor. J Biol Chem 278: 36396-36402
13. Dai S, Zhang Z, Chen S, Beachy RN (2004) RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease. Proc Natl Acad Sci USA 101: 687-692
14. de Vetten NC, Ferl RJ (1995) Characterization of a maize G-box binding factor that is induced by hypoxia. Plant J 7: 589-601
15. 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
16. 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
17. Fassler J, Landsman D, Acharya A, Moll JR, Bonovich M, Vinson C (2002) B-ZIP proteins encoded by the Drosophila genome: evaluation of potential dimerization partners. Genome Res 12: 1190-1200
18. Foster R, Izawa T, Chua NH (1994) Plant bZIP proteins gather at ACGT elements. FASEB J 8: 192-200
19. Fujita Y, Fujita M, Satoh R, Maruyama K, Parvez MM, Seki M, Hiratsu K, Ohme-Takagi M, Shinozaki K, Yamaguchi-Shinozaki K (2005) AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell 17:3470-3488
20. Fukazawa J, Sakai T, Ishida S, Yamaguchi I, Kamiya Y, Takahashi Y (2000) Repression of shoot growth, a bZIP transcriptional activator, regulates cell elongation by controlling the level of gibberellins. Plant Cell 12: 901-915
21. Hobo T, Asada M, Kowyama Y, Hattori T (1999b) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent. Plant J 19: 679-689
22. Hobo T, Kowyama Y, Hattori T (1999a) A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription. Proc Natl Acad Sci USA 96: 15348-15353
23. Holm M, Hardtke CS, Gaudet R, Deng XW (2001) Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. EMBO J 20: 118-127
24. 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. Genes Dev 16: 1247-1259
25. Hurst HC (1994) Transcription factors. 1: bZIP proteins. Protein Profile 1: 123-168
26. Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biol 47: 377-403
27. Itoh J, Nonomura K, Ikeda K, Yamaki S, Inukai Y, Yamagishi H, Kitano H, Nagato Y (2005) Rice plant development: from zygote to spikelet. Plant Cell Physiol 46: 23-47
28. Izawa T, Foster R, Chua NH (1993) Plant bZIP protein DNA binding specificity. J Mol Biol 230: 1131-1144
29. Izawa T, Foster R, Nakajima M, Shimamoto K, Chua NH (1994) The rice bZIP transcriptional activator RITA-1 is highly expressed during seed development. Plant Cell 6: 1277-1287
30. Jain M, Khurana P, Tyagi AK, Khurana JP (2008) Genome-wide analysis of intronless genes in rice and Arabidopsis. Funct Integr Genomics 8: 69-78
31. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483
32. Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of house-keeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345: 646-651
33. Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7: 106-111
34. Jiao Y, Ma L, Strickland E, Deng XW (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239-3256
35. Katagiri F, Lam E, Chua NH (1989) Two tobacco DNA-binding proteins with homology to the nuclear factor CREB. Nature 340: 727-730
36. 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
37. Lohmer S, Maddaloni M, Motto M, Di Fonzo N, Hartings H, Salamini F, Thompson RD (1991) The maize regulatory locus Opaque-2 encodes a DNA-binding protein which activates the transcription of the b-32 gene. EMBO J 10: 617-624
38. Lopez-Molina L, Mongrand S, McLachlin DT, Chait BT, Chua NH (2002) ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. Plant J 32: 317-328
39. Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, et al (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15: 1274-1283
40. Mallappa C, Yadav V, Negi P, Chattopadhyay S (2006) A basic leucine zipper transcription factor, G-box-binding factor 1, regulates blue light-mediated photomorphogenic growth in Arabidopsis. J Biol Chem 281: 22190-22199
41. Martinez-Garcia JF, Moyano E, Alcocer MJ, Martin C (1998) Two bZIP proteins from Antirrhinum flowers preferentially bind a hybrid C-box/G-box motif and help to define a new sub-family of bZIP transcription factors. Plant J 13: 489-505
42. 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
43. Minami M, Huh GH, Yang P, Iwabuchi M (1993) Coordinate gene expression of five subclass histones and the putative transcription factors, HBP-1a and HBP-1b, of histone genes in wheat. Plant Mol Biol 23: 429-434
44. Muszynski MG, Dam T, Li B, Shirbroun DM, Hou Z, Bruggemann E, Archibald R, Ananiev EV, Danilevskaya ON (2006) delayed flowering1 encodes a basic leucine zipper protein that mediates floral inductive signals at the shoot apex in maize. Plant Physiol 142: 1523-1536
45. Nakagawa H, Ohmiya K, Hattori T (1996) A rice bZIP protein, designated OSBZ8, is rapidly induced by abscisic acid. Plant J 9: 217-227
46. 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
47. Nantel A, Quatrano RS (1996) Characterization of three rice basic/leucine zipper factors, including two inhibitors of EmBP-1 DNA binding activity. J Biol Chem 271: 31296-31305
48. Niggeweg R, Thurow C, Kegler C, Gatz C (2000) Tobacco transcription factor TGA2.2 is the main component of as-1-binding factor ASF-1 and is involved in salicylic acid- and auxin-inducible expression of as-1-containing target promoters. J Biol Chem 275: 19897-19905
49. Nishimura R, Ohmori M, Fujita H, Kawaguchi M (2002) A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation. Proc Natl Acad Sci USA 99: 15206-15210
50. Niu X, 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
51. Okanami M, Meshi T, Tamai H, Iwabuchi M (1996) HALF-1, a bZIP-type protein, interacting with the wheat transcription factor HBP-1a contains a novel transcriptional activation domain. Genes Cells 1: 87-99
52. Onate L, Vicente-Carbajosa J, Lara P, Diaz I, Carbonero P (1999) Barley BLZ2, a seed-specific bZIP protein that interacts with BLZ1 in vivo and activates transcription from the GCN4-like motif of B-hordein promoters in barley endosperm. J Biol Chem 274: 9175-9182
53. Ono A, Izawa T, Chua NH, Shimamoto K (1996) The rab16B promoter of rice contains two distinct abscisic acid-responsive elements. Plant Physiol 112: 483-491
54. Onodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F (2001) A rice functional transcriptional activator, RISBZ1, responsible for endospermspecific expression of storage protein genes through GCN4 motif. J Biol Chem 276: 14139-14152
55. O'Shea EK, Rutkowski R, Kim PS (1992) Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68: 699-708
56. Patthy L (1987) Intron-dependent evolution: preferred types of exons and introns. FEBS Lett 214: 1-7
57. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, et al (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105-2110
58. Ringli C, Keller B (1998) Specific interaction of the tomato bZIP transcription factor VSF-1 with a non-palindromic DNA sequence that controls vascular gene expression. Plant Mol Biol 37: 977-988
59. Rodriguez-Uribe L, O'Connell MA (2006) A root-specific bZIP transcription factor is responsive to water deficit stress in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris). J Exp Bot 57: 1391-1398
60. Schindler U, Menkens AE, Beckmann H, Ecker JR, Cashmore AR (1992a) Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. EMBO J 11: 1261-1273
61. Schindler U, Terzaghi W, Beckmann H, Kadesch T, Cashmore AR (1992b) DNA binding site preferences and transcriptional activation properties of the Arabidopsis transcription factor GBF1. EMBO J 11: 1275-1289
62. Schmidt RJ, Ketudat M, Aukerman MJ, Hoschek G (1992) Opaque-2 is a transcriptional activator that recognizes a specific target site in 22-kD zein genes. Plant Cell 4: 689-700
63. 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
64. Strathmann A, Kuhlmann M, Heinekamp T, Droge-Laser W (2001) BZI-1 specifically heterodimerises with the tobacco bZIP transcription factors BZI-2, BZI-3/TBZF and BZI-4, and is functionally involved in flower development. Plant J 28: 397-408
65. Suckow M, von Wilcken-Bergmann B, Muller-Hill B (1993a) 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
66. Suckow M, von Wilcken-Bergmann B, Muller-Hill B (1993b) The DNA binding specificity of the basic region of the yeast transcriptional activator GCN4 can be changed by substitution of a single amino acid. Nucleic Acids Res 21: 2081-2086
67. Thomas D, Jacquemin I, Surdin-Kerjan Y (1992) MET4, a leucine zipper protein, and centromere-binding factor 1 are both required for transcriptional activation of sulfur metabolism in Saccharomyces cerevisiae. Mol Cell Biol 12: 1719-1727
68. Thurow C, Schiermeyer A, Krawczyk S, Butterbrodt T, Nickolov K, Gatz C (2005) Tobacco bZIP transcription factor TGA2.2 and related factor TGA2.1 have distinct roles in plant defense responses and plant development. Plant J 44: 100-113
69. Vicente-Carbajosa J, Onate L, Lara P, Diaz I, Carbonero P (1998) Barley BLZ1: a bZIP transcriptional activator that interacts with endospermspecific gene promoters. Plant J 13: 629-640
70. Vinson C, Myakishev M, Acharya A, Mir AA, Moll JR, Bonovich M (2002) Classification of human B-ZIP proteins based on dimerization properties. Mol Cell Biol 22: 6321-6335
71. Walsh J, Freeling M (1999) The liguleless2 gene of maize functions during the transition from the vegetative to the reproductive shoot apex. Plant J 19: 489-495
72. Wigge PA, Kim MC, Jaeger KE, Busch W, Schmid M, Lohmann JU, Weigel D (2005) Integration of spatial and temporal information during floral induction in Arabidopsis. Science 309: 1056-1059
73. Yamamoto MP, Onodera Y, Touno SM, Takaiwa F (2006) Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Plant Physiol 141: 1694-1707
74. Yang D, Wu L, Hwang YS, Chen L, Huang N (2001) Expression of the REB transcriptional activator in rice grains improves the yield of recombinant proteins whose genes are controlled by a Reb-responsive promoter. Proc Natl Acad Sci USA 98: 11438-11443
75. Yin Y, Chen L, Beachy R (1997a) Promoter elements required for phloem-specific gene expression from the RTBV promoter in rice. Plant J 12: 1179-1188
76. Yin Y, Zhu Q, Dai S, Lamb C, Beachy RN (1997b) RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development. EMBO J 16: 5247-5259
77. Zhang Y, Tessaro MJ, Lassner M, Li X (2003) Knockout analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance. Plant Cell 15: 2647-2653