Common mechanisms regulating expression of rice aleurone genes that contribute to the primary response for gibberellin

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1759, Issue 10, 2006, Pages 478-490

  Washio, Kenji ^a   Morikawa, Masaaki ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Aleurone; DNA methylation; GAMyb; Gibberellin; Rice; Seed germination

Indexed keywords

ARABIDOPSIS AGAMOUS PROTEIN; DNA; GIBBERELLIN; HISTONE;

ALEURONE; ARABIDOPSIS; ARTICLE; CHROMATIN; DNA METHYLATION; DNA MODIFICATION; GENE CONTROL; GENE EXPRESSION; GENE LOCUS; GENE SILENCING; GERMINATION; HOMEOBOX; INTRON; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; RICE;

BASE SEQUENCE; DNA METHYLATION; DNA, PLANT; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GIBBERELLINS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PROMOTER REGIONS (GENETICS); REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ARABIDOPSIS; ORYZA SATIVA;

EID: 33751199357     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbaexp.2006.09.001     Document Type: Article

References (78)

1. Hooley R. Gibberellins: perception, transduction and responses. Plant Mol. Biol. 26 (1994) 1529-1555
2. Olszewski N., Sun T.P., and Gubler F. Gibberellin signaling: biosynthesis, catabolism, and response pathways. Plant Cell 14 (2002) S61-S80
3. Ross J.J., Merfet I.C., and Reid J.B. Gibberellin mutants. Physiol. Plant. 100 (1997) 550-560
4. Sun T.P. Gibberellin signal transduction. Curr. Opin. Plant Biol. 3 (2000) 374-380
5. Thomas S.G., and Sun T.P. Update on gibberellin signaling. A tale of the tall and the short. Plant Physiol. 135 (2004) 668-676
6. Silverstone A.L., Jung H.S., Dill A., Kawaide H., Kamiya Y., and Sun T.P. Repressing a repressor: gibberellin-induced rapid reduction of the RGA protein in Arabidopsis. Plant Cell 13 (2001) 1555-1566
7. Itoh H., Ueguchi-Tanaka M., Sato Y., Ashikari M., and Matsuoka M. The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in nuclei. Plant Cell 14 (2002) 57-70
8. Gubler F., Chandler P.M., White R.G., Llewellyn D.J., and Jacobsen J.V. Gibberellin signaling in barley aleurone cells. Control of SLN1 and GAMYB expression. Plant Physiol. 129 (2002) 191-200
9. Ikeda A., Ueguchi-Tanaka M., Sonoda Y., Kitano H., Koshioka M., Futsuhara Y., Matsuoka M., and Yamaguchi J. Slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 13 (2001) 999-1010
10. Chandler P.M., Marion-Poll A., Ellis M., and Gubler F. Mutants at the Slender1 locus of barley cv. Himalaya. Molecular and physiological characterization. Plant Physiol. 129 (2002) 181-190
11. Peng J., Carol P., Richards D.E., King K.E., Cowling R.J., Murphy G.P., and Harberd N.P. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 11 (1997) 3194-3205
12. Dill A., Jung H.S., and Sun T.P. The DELLA motif is essential for gibberellin-induced degradation of RGA. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 14162-14167
13. Fleet C.M., and Sun T.P. A DELLAcate balance: the role of gibberellin in plant morphogenesis. Curr. Opin. Plant Biol. 8 (2005) 77-85
14. Deshaies R.J. SCF and Cullin/Ring H2-based ubiquitin ligases. Annu. Rev. Cell Dev. Biol. 15 (1999) 435-467
15. McGinnis K.M., Thomas S.G., Soule J.D., Strader L.C., Zale J.M., Sun T.P., and Steber C.M. The Arabidopsis SLEEPY1 gene encodes a putative F-box subunit of an SCF E3 ubiquitin ligase. Plant Cell 15 (2003) 1120-1130
16. Sasaki A., Itoh H., Gomi K., Ueguchi-Tanaka M., Ishiyama K., Kobayashi M., Jeong D.H., An G., Kitano H., Ashikari M., and Matsuoka M. Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299 (2003) 1896-1898
17. Ueguchi-Tanaka M., Ashikari M., Nakajima M., Itoh H., Katoh E., Kobayashi M., Chow T.Y., Hsing Y.I., Kitano H., Yamaguchi I., and Matsuoka M. GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437 (2005) 693-698
18. Peng J., Richards D.E., Hartley N.M., Murphy G.P., Devos K.M., Flintham J.E., Beales J., Fish L.J., Worland A.J., Pelica F., Sudhakar D., Christou P., Snape J.W., Gale M.D., and Harberd N.P. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400 (1999) 256-261
19. Dill A., and Sun T.P. Synergistic derepression of gibberellin signaling by removing RGA and GAI function in Arabidopsis thaliana. Genetics 159 (2001) 777-785
20. Lee S., Cheng H., King K.E., Wang W., He Y., Hussain A., Lo J., Harberd N.P., and Peng J. Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes Dev. 16 (2002) 646-658
21. King K.E., Moritz T., and Harberd N.P. Gibberellins are not required for normal stem growth in Arabidopsis thaliana in the absence of GAI and RGA. Genetics 159 (2001) 767-776
22. Wen C.K., and Chang C. Arabidopsis RGL1 encodes a negative regulator of gibberellin responses. Plant Cell 14 (2002) 87-100
23. Tyler L., Thomas S.G., Hu J., Dill A., Alonso J.M., Ecker J.R., and Sun T.P. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 135 (2004) 1008-1019
24. Cheng H., Qin L., Lee S., Fu X., Richards D.E., Cao D., Luo D., Harberd N.P., and Peng J. Gibberellin regulates Arabidopsis floral development via suppression of DELLA protein function. Development 131 (2004) 1055-1064
25. Murray F., Kalla R., Jacobsen J., and Gubler F. A role for HvGAMYB in anther development. Plant J. 33 (2003) 481-491
26. Lovegrove A., and Hooley R. Gibberellin and abscisic acid signalling in aleurone. Trends Plant Sci. 5 (2000) 102-110
27. Gubler F., Kalla R., Roberts J.K., and Jacobsen J.V. Gibberellin-regulated expression of a myb gene in barley aleurone cells: evidence for Myb transactivation of a high-pI α-amylase gene promoter. Plant Cell 7 (1995) 1879-1891
28. Kaneko M., Inukai Y., Ueguchi-Tanaka M., Itoh H., Izawa T., Kobayashi Y., Hattori T., Miyao A., Hirochika H., Ashikari M., and Matsuoka M. Loss-of-function mutations of the rice GAMYB gene impair α-amylase expression in aleurone and flower development. Plant Cell 16 (2004) 33-44
29. Washio K., and Ishikawa K. Structure and expression during the germination of rice seeds of the gene for a carboxypeptidase. Plant Mol. Biol. 19 (1992) 631-640
30. Rogers S.O., and Bendrich A.J. Extraction of DNA from milliguram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. 5 (1985) 69-76
31. Picard V., Ersdal-Badju E., Lu A., and Bock S.C. A rapid and efficient one-tube PCR-based mutagenesis technique using Pfu DNA polymerase. Nucleic Acids Res. 22 (1994) 2587-2591
32. Washio K. Identification of Dof proteins with implication in the gibberellin-regulated expression of a peptidase gene following the germination of rice grains. Biochim. Biophys. Acta 1520 (2001) 54-62
33. Washio K. Functional dissections between GAMYB and Dof transcription factors suggest a role for protein-protein associations in the gibberellin-mediated expression of the RAmy1A gene in the rice aleurone. Plant Physiol. 33 (2003) 850-863
34. Jacobsen S.E., Sakai H., Finnegan E.J., Cao X., and Meyerowitz E.M. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr. Biol. 10 (2000) 179-186
35. Gubler F., Watts R.J., Kalla R., Matthews P., Keys M., and Jacobsen J.V. Cloning of a rice cDNA encoding a transcription factor homologous to barley GAMyb. Plant Cell Physiol. 38 (1997) 362-365
36. O'Neill S.D., Kumagai M.H., Majumdar A., Huang N., Sutliff T.D., and Rodriguez R.L. The α-amylase genes in Oryza sativa: characterization of cDNA clones and mRNA expression during seed germination. Mol. Gen. Genet. 221 (1990) 235-244
37. Kaneko M., Itoh H., Inukai Y., Sakamoto T., Ueguchi-Tanaka M., Ashikari M., and Matsuoka M. Where do gibberellin biosynthesis and gibberellin signaling occur in rice plants?. Plant J. 35 (2003) 104-115
38. Kaneko M., Ashikari M., and Matsuoka M. Mapping and expression of rice GAMYB. Rice Genet. Newslett. 19 (2002) 24
39. Gomez-Cadenas A., Zentella R., Walker-Simmons M.K., and Ho T.H. Gibberellin/abscisic acid antagonism in barley aleurone cells: site of action of the protein kinase PKABA1 in relation to gibberellin signaling molecules. Plant Cell 13 (2001) 667-679
40. Benfey P.N., Ren L., and Chua N.H. The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns. EMBO J. 8 (1989) 2195-2202
41. Bradley D., Carpenter R., Sommer H., Hartley N., and Coen E. Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the plena locus of Antirrhinum. Cell 72 (1993) 85-95
42. Deyholos M.K., and Sieburth L.E. Separable whorl-specific expression and negative regulation by enhancer elements within the AGAMOUS second intron. Plant Cell 12 (2000) 1799-1810
43. Sheldon C.C., Conn A.B., Dennis E.S., and Peacock W.J. Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression. Plant Cell 14 (2002) 2527-2537
44. Simpson G.G. The autonomous pathway: epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time. Curr. Opin. Plant Biol. 7 (2004) 570-574
45. Tariq M., and Paszkowski J. DNA and histone methylation in plants. Trends Genet. 20 (2004) 244-251
46. Mantovani R. A survey of 178 NF-Y binding CCAAT boxes. Nucleic Acids Res. 26 (1998) 1135-1143
47. Mantovani R. The molecular biology of the CCAAT-binding factor NF-Y. Gene 239 (1999) 15-27
48. Gusmaroli G., Tonelli C., and Mantovani R. Regulation of the CCAAT-Binding NF-Y subunits in Arabidopsis thaliana. Gene 264 (2001) 173-185
49. Gusmaroli G., Tonelli C., and Mantovani R. Regulation of novel members of the Arabidopsis thaliana CCAAT-binding nuclear factor Y subunits. Gene 283 (2002) 41-48
50. Yang J., Xie Z., and Glover B.J. Asymmetric evolution of duplicate genes encoding the CCAAT-binding factor NF-Y in plant genomes. New Phytol. 165 (2005) 623-631
51. Ben-Naim O., Eshed R., Parnis A., Teper-Bamnolker P., Shalit A., Coupland G., Samach A., and Lifschitz E. The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA. Plant J. 46 (2006) 462-476
52. Lehmann M. Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure. Trends Genet. 20 (2004) 15-22
53. Farkas G., Gausz J., Galloni M., Reuter G., Gyurkovics H., and Karch F. The Trithorax-like gene encodes the Drosophila GAGA factor. Nature 371 (1994) 806-808
54. Kennison J.A. The Polycomb and trithorax group proteins of Drosophila: trans-regulators of homeotic gene function. Annu. Rev. Genet. 29 (1995) 289-303
55. Simon J.A., and Tamkun J.W. Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. Curr. Opin. Genet. Dev. 12 (2002) 210-218
56. Sangwan I., and O'Brian M.R. Identification of a soybean protein that interacts with GAGA element dinucleotide repeat DNA. Plant Physiol. 129 (2002) 1788-1794
57. Meister R.J., Williams L.A., Monfared M.M., Gallagher T.L., Kraft E.A., Nelson C.G., and Gasser C.S. Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter. Plant J. 37 (2004) 426-438
58. Santi L., Wang Y., Stile M.R., Berendzen K., Wanke D., Roig C., Pozzi C., Muller K., Muller J., Rohde W., and Salamini F. The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J. 34 (2003) 813-826
59. Kooiker M., Airoldi C.A., Losa A., Manzotti P.S., Finzi L., Kater M.M., and Colombo L. BASIC PENTACYSTEINE1, a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK. Plant Cell 17 (2005) 722-729
60. Le Hir H., Nott A., and Moore M.J. How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28 (2003) 215-220
61. Rose A.B. The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J. 40 (2004) 744-751
62. Sieburth L.E., and Meyerowitz E.M. Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 9 (1997) 355-365
63. Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A., and Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427 (2004) 164-167
64. Zhao Z., Yu Y., Meyer D., Wu C., and Shen W.H. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat. Cell Biol. 7 (2005) 1156-1160
65. Schubert D., Clarenz O., and Goodrich J. Epigenetic control of plant development by Polycomb-group proteins. Curr. Opin. Plant Biol. 8 (2005) 553-561
66. Chan S.W., Henderson I.R., and Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev., Genet. 6 (2005) 351-360
67. Cao X., and Jacobsen S.E. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 16491-16498
68. Cao X., and Jacobsen S.E. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12 (2002) 1138-1144
69. Lindroth A.M., Cao X., Jackson J.P., Zilberman D., McCallum C.M., Henikoff S., and Jacobsen S.E. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292 (2001) 2077-2080
70. Lindroth A.M., Shultis D., Jasencakova Z., Fuchs J., Johnson L., Schubert D., Patnaik D., Pradhan S., Goodrich J., Schubert I., Jenuwein T., Khorasanizadeh S., and Jacobsen S.E. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23 (2004) 4286-4296
71. Jackson J.P., Lindroth A.M., Cao X., and Jacobsen S.E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416 (2002) 556-560
72. Itoh H., Sasaki A., Ueguchi-Tanaka M., Ishiyama K., Kobayashi M., Hasegawa Y., Minami E., Ashikari M., and Matsuoka M. Dissection of the phosphorylation of rice DELLA protein, SLENDER RICE1. Plant Cell Physiol. 46 (2005) 1392-1399
73. Ikeda A., Sonoda Y., Vernieri P., Perata P., Hirochika H., and Yamaguchi J. The slender rice mutant, with constitutively activated gibberellin signal transduction, has enhanced capacity for abscisic acid level. Plant Cell Physiol. 43 (2002) 974-979
74. Itoh H., Shimada A., Ueguchi-Tanaka M., Kamiya N., Hasegawa Y., Ashikari M., and Matsuoka M. Overexpression of a GRAS protein lacking the DELLA domain confers altered gibberellin responses in rice. Plant J. 44 (2005) 669-679
75. Kaneko M., Itoh H., Ueguchi-Tanaka M., Ashikari M., and Matsuoka M. The α-amylase induction in endosperm during rice seed germination is caused by gibberellin synthesized in epithelium. Plant Physiol. 128 (2002) 1264-1270
76. Mena M., Cejudo F.J., Isabel-Lamoneda I., and Carbonero P. A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiol. 130 (2002) 111-119
77. Mena M., Vicente-Carbajosa J., Schmidt R.J., and Carbonero P. An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm. Plant J. 16 (1998) 53-62
78. Radchuk V.V., Sreenivasulu N., Radchuk R.I., Wobus U., and Weschke W. The methylation cycle and its possible functions in barley endosperm development. Plant Mol. Biol. 59 (2005) 289-307