Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa)

Plant Molecular Biology

Volumn 62, Issue 1-2, 2006, Pages 233-246

  Ross, Christian ^a   Shen, Qingxi J ^a  

^a UNIVERSITY OF NEVADA   (United States)

Author keywords

Abscisic acid; Bioinformatics; Computational modeling; Genome; Oryza sativa; Rice

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL MODELING; ORYZA SATIVA; PUTATIVE REGULATORY GENES;

CARBOXYLIC ACIDS; COMPUTATIONAL METHODS; HORMONES; PLANTS (BOTANY);

CROPS;

ABSCISIC ACID; HVA1 PROTEIN, HORDEUM VULGARE; PHYTOHORMONE; VEGETABLE PROTEIN;

ARTICLE; BARLEY; BIOLOGICAL MODEL; DRUG EFFECT; GENETICS; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE;

ABSCISIC ACID; BASE SEQUENCE; HORDEUM; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; ORYZA SATIVA; PLANT GROWTH REGULATORS; PLANT PROTEINS; PROMOTER REGIONS (GENETICS); PROMOTER REGIONS, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ABSCISIC ACID; CARBOXYLIC ACIDS; COMPUTATION; FARM CROPS; HORMONES; PLANTS; RICE;

HORDEUM VULGARE SUBSP. VULGARE; ORYZA SATIVA;

EID: 33748543644     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-006-9017-y     Document Type: Article

References (73)

1. Alvarado MC, Zsigmond LM, Kovacs I, Cseplo A, Koncz C, Szabados LM (2004) Gene trapping with firefly luciferase in Arabidopsis. tagging of stress-responsive genes. Plant Physiol 134:18-27
2. Aneeta, Sanan-Mishra N, Tuteja N, Kumar Sopory S (2002) Salinity- and ABA-induced up-regulation and light-mediated modulation of mRNA encoding glycine-rich RNA-binding protein from Sorghum bicolor. Biochem Biophys Res Commun 296:1063-1068
3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25-29
4. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp 28-36
5. Blackwood EM, Kadonaga JT (1998) Going the distance: a current view of enhancer action. Science 281:60-63
6. Carles C, Bies-Etheve N, Aspart L, Leon-Kloosterziel KM, Koornneef M, Echeverria M, Delseny M (2002) Regulation of Arabidopsis thaliana Em genes: role of ABI5. Plant J 30:373-383
7. Casaretto J, Ho T-hD (2003) The transcription factors HvABI5 and HvVP1 are required for the abscisic acid induction of gene expression in barley aleurone cells. Plant Cell 15:271-284
8. Casaretto JA, Ho T-hD (2005) Transcriptional regulation by abscisic acid in barley (Hordeum vulgare L.) seeds involves autoregulation of the transcription factor HvABI5. Plant Mol Biol 57:21-34
9. Chinnusamy V, Schumaker K, Zhu JK (2004) Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J Exp Bot 55:225-236
10. Cutler AJ, Krochko JE (1999) Formation and breakdown of ABA. Trends Plant Sci 4:472-478
11. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342-1353
12. Dunford RP, Kurata N, Laurie DA, Money TA, Minobe Y, Moore G (1995) Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucleic Acids Res 23:2724-2728
13. Enyedi AJ, Raskin I (1993) Induction of UDP-glucose:salicylic acid glucosyltransferase activity in tobacco mosaic virus-inoculated tobacco (Nicotiana tabacum) leaves. Plant Physiol 101:1375-1380
14. Fan LM, Zhao Z, Assmann SM (2004) Guard cells: a dynamic signaling model. Curr Opin Plant Biol 7:537-546
15. Finkelstein RR, Gampala SS, Rock CD (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell 14: S15-S45
16. Finkelstein RR, Rock CD (2002) Abscisic acid biosynthesis and response. The Arabidopsis Book. In: Somerville CR, Meyerowitz EM (eds) American Society of Plant Biologists, pp 1-48
17. Giraudat J, Parcy F, Bertauche N, Gosti F, Leung J, Morris PC, Bouvier-Durand M, Vartanian N (1994) Current advances in abscisic acid action and signalling. Plant Mol Biol 26:1557-1577
18. Groth D, Lehrach H, Hennig S (2004) GOblet: a platform for gene ontology annotation of anonymous sequence data. Nucl Acids Res 32: W313-W317
19. Hare PD, Seo HS, Yang JY, Chua NH (2003) Modulation of sensitivity and selectivity in plant signaling by proteasomal destabilization. Curr Opin Plant Biol 6:453-462
20. Hattori T, Totsuka M, Hobo T, Kagaya Y, Yamamoto-Toyoda A (2002) Experimentally determined sequence requirement of ACGT-containing abscisic acid response element. Plant Cell Physiol 43:136-140
21. Himmelbach A, Yang Y, Grill E (2003) Relay and control of abscisic acid signaling. Curr Opin Plant Biol 6:470-479
22. Hirose T, Sugita M, Sugiura M (1993) cDNA structure, expression and nucleic acid-binding properties of three RNA-binding proteins in tobacco: occurrence of tissue-specific alternative splicing. Nucleic Acids Res 21:3981-3987
23. Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent. Plant J 19:679-689
24. Hobo T, Kowyama Y, Hattori T (1999) A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription. PNAS 96:15348-15353
25. Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biolgy 47:377-403
26. Jones AL, Quimby BB, Hood JK, Ferrigno P, Keshava PH, Silver PA, Corbett AH (2000) SAC3 may link nuclear protein export to cell cycle progression. PNAS 97:3224-3229
27. Joshee N, Kisaka H, Kitagawa Y (1998) Isolation and characterization of a water stress-specific genomic gene, pwsi18, from rice. Plant Cell Physiol 39:64-72
28. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashidume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376-379
29. Kong J, Gong JM, Zhang ZG, Zhang JS, Chen SY (2003) A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress. Theor Appl Genet 107:326-331
30. Koornneef M, Reuling G, Karssen CM (1984) The Isolation and characterization of abscisic-acid insensitive mutants of Arabidopsis thaliana. Physiol Plantarum 61:377-383
31. Kuhn JM, Schroeder JI (2003) Impacts of altered RNA metabolism on abscisic acid signaling. Curr Opin Plant Biol 6:463-469
32. Kuwabara C, Arakawa K, Yoshida S (1999) Abscisic acid-induced secretory proteins in suspension-cultured cells of winter wheat. Plant Cell Physiol 40:184-191
33. Kuwabara C, Takezawa D, Shimada T, Hamada T, Fujikawa S, Arakawa K (2002) Abscisic acid- and cold-induced thaumatin-like protein in winter wheat has an antifungal activity against snow mould, Microdochium nivale. Physiol Plantarum 115:101-110
34. Leung J, Giraudat J (1998) Abscisic acid signal transduction. Annu Rev Plant Physiol Plant Mol Biol 49:199-222
35. Lovegrove A, Hooley R (2000) Gibberellin and abscisic acid signalling in aleurone. Trends Plant Sci 5:102-110
36. Mahalingam R, Gomez-Buitrago A, Eckardt N, Shah N, Guevara-Garcia A, Day P, Raina R, Fedoroff NV (2003) Characterizing the stress/defense transcriptome of Arabidopsis. Genome Biol 4: R20
37. Mauch-Mani B, Mauch F (2005) The role of abscisic acid in plant-pathogen interactions. Curr Opin Plant Biol 8:409-414
38. Moons A, De Keyser A, Van Montagu M (1997) A group 3 LEA cDNA of rice, responsive to abscisic acid, but not to jasmonic acid, shows variety-specific differences in salt stress response. Gene 191:197-204
39. Morris PC, Kumar A, Bowles DJ, Cuming AC (1990) Osmotic stress and abscisic acid induce expression of the wheat Em genes. Eur J Biochem 190:625-630
40. Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J: For Cell Mol Biol 34:137-148
41. Narusaka Y, Narusaka M, Seki M, Umezawa T, Ishida J, Nakajima M, Enju A, Shinozaki K (2004) Crosstalk in the responses to abiotic and biotic stresses in Arabidopsis: analysis of gene expression in cytochrome P450 gene superfamily by cDNA microarray. Plant Mol Biol 55:327-342
42. Nicolas C, Rodriguez D, Poulsen F, Eriksen EN, Nicolas G (1997) The expression of an abscisic acid-responsive glycinerich protein coincides with the level of seed dormancy in Fagus sylvatica. Plant Cell Physiol 38:1303-1310
43. Niu X, Helentjaris T, Bate NJ (2002) Maize ABI4 binds Coupling Element1 in abscisic acid and sugar response genes. Plant Cell 14:2565-2575
44. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. PNAS 85:2444-2448
45. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucl Acids Res 29:e45-
46. Pieterse CM, Van Loon L (2004) NPR1: the spider in the web of induced resistance signaling pathways. Curr Opin Plant Biol 7:456-464
47. Porter T, Coon M (1991) Cytochrome P-450. Multiplicity of isoforms, substrates, and catalytic and regulatory mechanisms. J Biol Chem 266:13469-13472
48. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755-1767
49. Razem FA, El-Kereamy A, Abrams SR, Hill RD (2006) The RNA-binding protein FCA is an abscisic acid receptor. Nature 439:290-294
50. Ritchie SM, Swanson SJ, Gilroy S (2002) From common signalling components to cell specific responses: insights from the cereal aleurone. Physiol Plant 115:342-351
51. Rock CD (2000) Pathways to abscisic acid-regulated gene expression. New Phytol 148:357-396
52. Schroeder JI, Allen GJ, Hugouvieux V, Kwak JM, Waner D (2001) Guard cell signal transduction. Annu Rev Plant Physiol Plant Mol Biol 52:627-658
53. Shen Q, Ho TH (1995) Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent ABA-responsive complexes each containing a G-box and a novel cis-acting element. Plant Cell 7:295-307
54. Shen Q, Uknes SJ, Ho THD (1993) Hormone response complex of a novel abscisic acid and cycloheximide inducible barley gene. J Biol Chem 268:23652-23660
55. Shen Q, Zhang P, Ho T (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufficient for ABA induction of gene expression in barley. Plant Cell 8:1107-1119
56. Shen QJ, Casaretto JA, Zhang P, Ho T-HD (2004) Functional definition of ABA-response complexes: the promoter units necessary and sufficient for ABA induction of gene expression in barley (Hordeum vulgare L.). Plant Mol Biol 54:111-124
57. Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Two different novel cisacting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence. Plant J 33:259-270
58. Stintzi A, Browse J (2000) The Arabidopsis male-sterile mutant, opr3, lacks the 12-oxophytodienoic acid reductase required for jasmonate synthesis. PNAS 97:10625-10630
59. Stintzi A, Heitz T, Prasad V, Wiedemann-Merdinoglu S, Kauffmann S, Geoffroy P, Legrand M, Fritig B (1993) Plant 'pathogenesis-related' proteins and their role in defense against pathogens. Biochimie 75:687-706
60. Su J, Shen Q, David Ho TH, Wu R (1998) Dehydration-stress-regulated transgene expression in stably transformed rice plants. Plant Physiol 117:913-922
61. Takahashi S, Seki M, Ishida J, Satou M, Sakurai T, Narusaka M, Kamiya A, Nakajima M, Enju A, Akiyama K, Yamaguchi-Shinozaki K, Shinozaki K (2004) Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray. Plant Mol Biol 56:29-55
62. Vick BA, Zimmerman DC (1986) Characterization of 12-oxophytodienoic acid reductase in corn. Plant Physiol 80:202-205
63. Xie Z, Ruas P, Shen QS (2005) The signaling networks of the phytohormone abscisic acid. In: Litwack G (eds) Vitamins and hormones. Elsevier, New York, pp 235-269
64. Xu Q, Belcastro MP, Villa ST, Dinkins RD, Clarke SG, Downie AB (2004) A second protein L-isoaspartyl methyltransferase gene in Arabidopsis produces two transcripts whose products are sequestered in the nucleus. Plant Physiol 136:2652-2664
65. Xue G-P, Loveridge CW (2004) HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element. Plant J 37:326-339
66. Yadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S (2005) A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Plant Cell: tpc.105.032060
67. Yamaguchi-Shinozaki K, Mundy J, Chua NH (1990) Four tightly linked rab genes are differentially expressed in rice. Plant Mol Biol 14:29-39
68. Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6:251-264
69. Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S (2004) Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol Genomics 17:87-100
70. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR (2005) The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Plant Physiol 138:18-26
71. Zhang W, Ruan J, Ho T-hD, You Y, Yu T, Quatrano RS (2005) cis-Regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana. Bioinformatics 21:3074-3081
72. Zhang Y, Wang L (2005) The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol 5:1
73. Zhang Z-L, Xie Z, Zou X, Casaretto J, Ho T-hD, Shen QJ (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol. 134:1500-1513