Coexpression analysis identifies rice starch regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator

Plant Physiology

Volumn 154, Issue 2, 2010, Pages 927-938

  Fu, Fang Fang ^a   Xue, Hong Wei ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ORYZA SATIVA;

EID: 77957724477     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.110.159517     Document Type: Article

References (44)

1. Akihiro T, Mizuno K, Fujimura T (2005) Gene expression of ADP-Glc pyrophosphorylase and starch contents in rice cultured cells are cooperatively regulated by Suc and ABA. Plant Cell Physiol 46: 937-946
2. Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48: 381-390
3. Bao J, Jin L, Xiao P, Shen S, Sun M, Corke H (2008) Starch physicochemical properties and their associations with microsatellite alleles of starchsynthesizing genes in a rice RIL population. J Agric Food Chem 56: 1589-1594
4. Bertoft E, Koch K (2000) Composition of chains in waxy-rice starch and its structural units. Carbohydr Polym 41: 121-132
5. Cai Y, Wang W, Zhu Z, Zhang Z, Yang J, Zhu Q (2006) The physiochemical characteristics of amylopectin and their relationships to pasting properties of rice flour in different varieties. Sci Agric Sin 39: 1122-1129
6. Cao H, Shannon JC (1997) Effect of gibberellin on growth, protein secretion, and starch accumulation in maize endosperm suspension cells. J Plant Growth Regul 16: 137-140
7. Dian W, Jiang H, Chen Q, Liu F, Wu P (2003) Cloning and characterization of the granule-bound starch synthase II gene in rice: gene expression is regulated by the nitrogen level, sugar and circadian rhythm. Planta 218: 261-268
8. Fu FF, Ye R, Xu SP, Xue HW (2009) Studies on rice seed quality through analysis of a large-scale T-DNA insertion population. Cell Res 19: 380-391
9. Fujita N, Kubo A, Suh DS, Wong KS, Jane JL, Ozawa K, Takaiwa F, Inaba Y, Nakamura Y (2003) Antisense inhibition of isoamylase alters the structure of amylopectin and the physicochemical properties of starch in rice endosperm. Plant Cell Physiol 44: 607-618
10. Fujita N, Yoshida M, Asakura N, Ohdan T, Miyao A, Hirochika H, Nakamura Y (2006) Function and characterization of starch synthase I using mutants in rice. Plant Physiol 140: 1070-1084
11. Fujita N, Yoshida M, Kondo T, Saito K, Utsumi Y, Tokunaga T, Nishi A, Satoh H, Park JH, Jane JL, et al (2007) Characterization of SSIIIadeficient mutants of rice: the function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm. Plant Physiol 144: 2009-2023
12. Gachon C, Mingam A, Charrier B (2004) Real-time PCR: what relevance to plant studies. J Exp Bot 55: 1445-1454
13. Gusmaroli G, Tonelli C, Mantovani R (2001) Regulation of the CCAATbinding NF-Y subunits in Arabidopsis thaliana. Gene 264: 173-185
14. Hanashiro I, Itoh K, Kuratomi Y, Yamazaki M, Igarashi T, Matsugasako J, Takeda Y (2008) Granule-bound starch synthase I is responsible for biosynthesis of extra-long unit chains of amylopectin in rice. Plant Cell Physiol 49: 925-933
15. Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6: 271-282
16. Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K, et al (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA 104: 6478-6483
17. Hizukuri S (1986) Polymodal distribution of the chain lengths of amylopectins and its significance. Carbohydr Res 147: 342-347
18. Ihmels J, Levy R, Barkai N (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22: 86-92
19. Jane J, Chen YY, Lee LF, McPherson AE, Wong KS, Radosavljevic M, Kasemsuwan T (1999) Effects of amylopectin branch chain length and amylose content on the gelatinization and pasting properties of starch. Cereal Chem 76: 629-637
20. Jofuku KD, Omidyar PK, Gee Z, Okamuro JK (2005) Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc Natl Acad Sci USA 102: 3117-3122
21. Juliano BO (1971) A simplified assay for milled-rice amylose. Cereal Sci Today 16: 334-340
22. Kim S, Soltis PS, Wall K, Soltis DE (2006) Phylogeny and domain evolution in the APETALA2-like gene family.Mol Biol Evol 23: 107-120
23. Lee DY, Lee J, Moon S, Park SY, An G (2007) The rice heterochronic gene SUPERNUMERARY BRACT regulates the transition from spikelet meristem to floral meristem. Plant J 49: 64-78
24. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res 14: 1085-1094
25. Li QF, Zhang GY, Dong ZW, Yu HX, Gu MH, Sun SS, Liu QQ (2009) Characterization of expression of the OsPUL gene encoding a pullulanase- type debranching enzyme during seed development and germination in rice. Plant Physiol Biochem 47: 351-358
26. Miyoshi K, Ito Y, Serizawa A, Kurata N (2003) OsHAP3 genes regulate chloroplast biogenesis in rice. Plant J 36: 532-540
27. Nagamine T, Komae K (1996) Improvement of a method for chain-length distribution analysis of wheat amylopectin. J Chromatogr A 732: 255-259
28. Nakamura Y, Francisco PB Jr, Hosaka Y, Sato A, Sawada T, Kubo A, Fujita N (2005) Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol 58: 213-227
29. Nishi A, Nakamura Y, Tanaka N, Satoh H (2001) Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. Plant Physiol 127: 459-472
30. Ohdan T, Francisco PB Jr, Sawada T, Hirose T, Terao T, Satoh H, Nakamura Y (2005) Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J Exp Bot 56: 3229-3244
31. Ohto MA, Fischer RL, Goldberg RB, Nakamura K, Harada JJ (2005) Control of seed mass by APETALA2. Proc Natl Acad Sci USA 102: 3123-3128
32. Okita TW, Sun J, Sakulringharoj C, Choi SB, Edwards GE, Kato C, Ito H, Matsui H (2001) Increasing rice productivity and yield by manipulation of starch synthesis. Novartis Found Symp 236: 135-152
33. Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102: 8633-8638
34. Rook F, Corke F, Card R, Munz G, Smith C, Bevan MW (2001) Impaired Suc-induction mutants reveal the modulation of sugar-induced starch biosynthetic gene expression by abscisic acid signalling. Plant J 26: 421-433
35. Satoh H, Nishi A, Yamashita K, Takemoto Y, Tanaka Y, Hosaka Y, Sakurai A, Fujita N, Nakamura Y (2003) Starch-branching enzyme I-deficient mutation specifically affects the structure and properties of starch in rice endosperm. Plant Physiol 133: 1111-1121
36. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
37. Smidansky ED, Martin JM, Hannah LC, Fischer AM, Giroux MJ (2003) Seed yield and plant biomass increases in rice are conferred by deregulation of endosperm ADP-Glu pyrophosphorylase. Planta 216: 656-664
38. Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D, et al (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106: 21760-21765
39. Turner DH, Turner JF (1960) The hydrolysis of Glc monophosphates by a phosphatase preparation from pea seeds. Biochem J 74: 486-491
40. Wu Z, Irizarry RA, Gentleman R (2004) A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 99: 909-917
41. Wuriyanghan H, Zhang B, Cao WH, Ma B, Lei G, Liu YF, Wei W, Wu HJ, Chen LJ, Chen HW, et al (2009) The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice. Plant Cell 21: 1473-1494
42. Xie YL (2006) AP2/EREBP: a special transcription factor family in plant. Journal of Qinghai Normal University 3: 80-83
43. Xue LJ, Zhang JJ, Xue HW (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 37: 916-930
44. Zhu Y, Cai XL, Wang ZY, Hong MM (2003) An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. J Biol Chem 278: 47803-47811