The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Huang, Jianyan ^a   Zhao, Xiaobo ^a   Weng, Xiaoyu ^a   Wang, Lei ^a   Xie, Weibo ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PHYTOHORMONE;

ARTICLE; B BOX ZINC FINGER GENE; BIOINFORMATICS; CHROMOSOMAL LOCALIZATION; CHROMOSOME DUPLICATION; CIRCADIAN RHYTHM; CULTIVAR; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE STRUCTURE; GENOME ANALYSIS; HORMONAL REGULATION; LIFE CYCLE; LIGHT DARK CYCLE; MICROARRAY ANALYSIS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; POLYMERASE CHAIN REACTION; PROTEIN DOMAIN; RICE; SEQUENCE ALIGNMENT;

ABSCISIC ACID; AMINO ACID SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CIRCADIAN RHYTHM; CONSENSUS SEQUENCE; ENHANCER ELEMENTS, GENETIC; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PHYLOGENY; PLANT GROWTH REGULATORS; PLANT PROTEINS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; TRANSCRIPTOME; ZINC FINGERS;

ARABIDOPSIS;

EID: 84868296559     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048242     Document Type: Article

References (57)

1. Gong W, Shen YP, Ma LG, Pan Y, Du YL, et al. (2004) Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol 135: 773-782.
2. Gao G, Zhong YF, Guo AY, Zhu QH, Tang W, et al. (2006) DRTF: a database of rice transcription factors. Bioinformatics 22: 1286-1287.
3. Khanna R, Kronmiller B, Maszle DR, Coupland G, Holm M, et al. (2009) The Arabidopsis B-box zinc finger family. Plant Cell 21: 3416-3420.
4. Klug A, Schwabe JW, (1995) Protein motifs 5. Zinc fingers. FASEB J 9: 597-604.
5. Putterill J, Robson F, Lee K, Simon R, Coupland G, (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80: 847-857.
6. Robson F, Costa MM, Hepworth SR, Vizir I, Pineiro M, et al. (2001) Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. Plant J 28: 619-631.
7. Borden KL, (1998) RING fingers and B-boxes: zinc-binding protein-protein interaction domains. Biochem Cell Biol 76: 351-358.
8. Torok M, Etkin LD, (2000) Two B or not two B? Overview of the rapidly expanding B-box family of proteins. Differentiation 67: 63-71.
9. Chang CS, Li YH, Chen LT, Chen WC, Hsieh WP, et al. (2008) LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant J 54: 205-219.
10. Kumagai T, Ito S, Nakamichi N, Niwa Y, Murakami M, et al. (2008) The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana. Biosci Biotechnol Biochem 72: 1539-1549.
11. Ledger S, Strayer C, Ashton F, Kay SA, Putterill J, (2001) Analysis of the function of two circadian-regulated CONSTANS-LIKE genes. Plant J 26: 15-22.
12. Datta S, Hettiarachchi GH, Deng XW, Holm M, (2006) Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. Plant Cell 18: 70-84.
13. Hassidim M, Harir Y, Yakir E, Kron I, Green RM, (2009) Over-expression of CONSTANS-LIKE 5 can induce flowering in short-day grown Arabidopsis. Planta 230: 481-491.
14. Cheng X-F, Wang Z-Y, (2005) Overexpression of COL9, a CONSTANS-LIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. Plant J 43: 758-768.
15. Wang QM, Zeng JX, Deng KQ, Tu XJ, Zhao XY, et al. (2011) DBB1a, involved in gibberellin homeostasis, functions as a negative regulator of blue light-mediated hypocotyl elongation in Arabidopsis. Planta 233: 13-23.
16. Indorf M, Cordero J, Neuhaus G, Rodríguez-Franco M, (2007) Salt tolerance (STO), a stress-related protein, has a major role in light signalling. Plant J 51: 563-574.
17. Holm M, Hardtke CS, Gaudet R, Deng X-W, (2001) Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. EMBO J 20: 118-127.
18. Datta S, Hettiarachchi C, Johansson H, Holm M, (2007) SALT TOLERANCE HOMOLOG2, a B-box protein in Arabidopsis that activates transcription and positively regulates light-mediated development. Plant Cell 19: 3242-3255.
19. Datta S, Johansson H, Hettiarachchi C, Irigoyen ML, Desai M, et al. (2008) LZF1/SALT TOLERANCE HOMOLOG3, an Arabidopsis B-box protein involved in light-dependent development and gene expression, undergoes COP1-mediated ubiquitination. Plant Cell 20: 2324-2338.
20. Chang C-SJ, Maloof JN, Wu S-H, (2011) COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol 156: 228-239.
21. Holtan HE, Bandong S, Marion CM, Adam L, Tiwari S, et al. (2011) BBX32, an Arabidopsis b-box protein, functions in light signaling by suppressing hy5-regulated gene expression and interacting with STH2/BBX21. Plant Physiol 156: 2109-2123.
22. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, et al. (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12: 2473-2484.
23. Kim SK, Yun CH, Lee JH, Jang YH, Park HY, et al. (2008) OsCO3, a CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of FT-like genes under SD conditions in rice. Planta 228: 355-365.
24. Griffiths S, Dunford RP, Coupland G, Laurie DA, (2003) The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131: 1855-1867.
25. Lee YS, Jeong DH, Lee DY, Yi J, Ryu CH, et al. (2010) OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. Plant J 63: 18-30.
26. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
27. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-887.
28. Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, et al. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 36: D1028-D1033.
29. Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, et al. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 17: 175-183.
30. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
31. Schultz J, Milpetz F, Bork P, Ponting CP, (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 95: 5857-5864.
32. Letunic I, Doerks T, Bork P, (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40: D302-305.
33. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-D301.
34. Guo AY, Zhu QH, Chen X, Luo JC, (2007) GSDS: a gene structure display server. Yi chuan 29: 1023-1026.
35. Voorrips RE, (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
36. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
37. Crooks GE, Hon G, Chandonia JM, Brenner SE, (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
38. Wang L, Xie W, Chen Y, Tang W, Yang J, et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 61: 752-766.
39. Zhao X, Huang J, Yu H, Wang L, Xie W, (2010) Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.). BMC Plant Biol 10: 92.
40. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
41. Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, et al. (2007) The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol 72: 353-363.
42. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, et al. (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14.
43. Xue W, Xing Y, Weng X, Zhao Y, Tang W, et al. (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40: 761-767.
44. Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, et al. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30: 325-327.
45. Zhang H, Jin J, Tang L, Zhao Y, Gu X, et al. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39: D1114-1117.
46. Perez-Rodriguez P, Riano-Pachon DM, Correa LGG, Rensing SA, Kersten B, et al. (2010) PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38: D822-D827.
47. Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, et al. (2011) In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. DNA Res 18: 321-332.
48. Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, et al. (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149: 171-180.
49. Gray J, Bevan M, Brutnell T, Buell CR, Cone K, et al. (2009) A recommendation for naming transcription factor proteins in the grasses. Plant Physiol 149: 4-6.
50. Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, et al. (2006) Decoding the rice genome. Bioessays 28: 421-432.
51. Paterson AH, Bowers JE, Chapman BA, (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101: 9903-9908.
52. Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38.
53. 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.
54. 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.
55. Casal JJ, Fankhauser C, Coupland G, Blázquez MA, (2004) Signalling for developmental plasticity. Trends Plant Sci 9: 309-314.
56. Santner A, Calderon-Villalobos LIA, Estelle M, (2009) Plant hormones are versatile chemical regulators of plant growth. Nat Chem Biol 5: 301-307.
57. Lau OS, Deng XW, (2010) Plant hormone signaling lightens up: integrators of light and hormones. Curr Opin Plant Biol 13: 571-577.