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Keiichi Kojima, Kohji Suzuki, Toshiki Taya, Mio Tonouchi, Charles Nelson, Allen
Nakagawa, Yasuhiro Otomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai,
Piero Carninci, Yoshihide Hayashizaki and Shoshi Kikuchi
Physiol Genomics 17:87-100, 2004. First published Feb 24, 2004;
doi:10.1152/physiolgenomics.00201.2003
This article cites 39 articles, 16 of which you can access free at:
http://physiolgenomics.physiology.org/cgi/content/full/17/2/87#BIBL
Global Patterns of Gene Expression in the Aleurone of Wild-Type and dwarf1 Mutant Rice
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http://physiolgenomics.physiology.org/cgi/content/full/17/2/87
Additional material and information about Physiological Genomics can be found at:
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Physiological Genomics publishes results of a wide variety of studies from human and from informative model systems with
techniques linking genes and pathways to physiology, from prokaryotes to eukaryotes. It is published quarterly in January, April,
July, and October by the American Physiological Society, 9650 Rockville Pike, Bethesda MD 20814-3991. Copyright © 2005 by
the American Physiological Society. ISSN: 1094-8341, ESSN: 1531-2267. Visit our website at http://www.the-aps.org/.
Physiol Genomics 17: 87–100, 2004.
First published February 24, 2004; 10.1152/physiolgenomics.00201.2003.
Yazaki, Junshi, Zenpei Shimatani, Akiko Hashimoto, Yuko genome-wide expression analysis; germination; dormancy; compara-
Nagata, Fumiko Fujii, Keiichi Kojima, Kohji Suzuki, Toshiki tive genomics; cis-element
Taya, Mio Tonouchi, Charles Nelson, Allen Nakagawa, Yasuhiro
Otomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero
Carninci, Yoshihide Hayashizaki, and Shoshi Kikuchi. Transcrip- RICE (Oryza sativa) is an important food crop that is useful as
tional profiling of genes responsive to abscisic acid and gibberellin in an experimental model because of its small genome size,
rice: phenotyping and comparative analysis between rice and Arabi- extensive genetic map, relative ease of transformation, and
dopsis. Physiol Genomics 17: 87–100, 2004. First published February synteny with other cereal crops. Draft sequences of the O.
24, 2004; 10.1152/physiolgenomics.00201.2003.—We collected and sativa L. ssp. indica (41) and japonica (8) genomes, obtained
completely sequenced 32,127 full-length complementary DNA clones
from Oryza sativa L. ssp. japonica cv. “Nipponbare.” Mapping of
by the whole-genome shotgun sequencing method, have been
these clones to genomic DNA revealed ⬃20,500 transcriptional units published. The National Institute of Agrobiological Sciences
(TUs) in the rice genome. For each TU, we selected 60-mers using an (NIAS) at Tsukuba, Japan, and its collaborators have con-
algorithm that took into account some DNA conditions such as base structed useful tools for functional genomics through the Rice
composition and sequence complexity. Using in situ synthesis tech- Genome Project of Japan. These tools consist of 32,127 full-
nology, we constructed oligonucleotide arrays with these TUs on glass length cDNA (FL-cDNA) clones (18), over 600 expression
slides. We targeted RNAs prepared from normally grown rice callus profiles developed by using an 8,987-cDNA microarray (39), a
and from callus treated with abscisic acid (ABA) or gibberellin (GA). high-quality genomic sequence that has 99.99% accuracy (5,
We identified 200 ABA-responsive and 301 GA-responsive genes, 32), a genetic map with 3,267 DNA markers (9), rice material
many of which had never before been annotated as ABA or GA for genetic analysis, and about 50,000 transposon insertion
responsive in other expression analysis. Comparison of these genes
revealed antagonistic regulation of almost all by both hormones; these
lines (24). All the information from these tools can be accessed
had previously been annotated as being responsible for protein storage through the Rice PIPELINE system (40). These tools may be
and defense against pathogens. Comparison of the cis-elements of important for improving not only rice but also other cereals,
genes responsive to one or antagonistic to both hormones revealed because functionally important sequences are conserved and
that the antagonistic genes had cis-elements related to ABA and GA may be identified by their synteny. Of these tools, the FL-
responses. The genes responsive to only one hormone were rich in cDNA clones, in particular, are necessary for the identification
cis-elements that supported ABA and GA responses. In a search for of exon-intron boundaries and gene-coding regions within
the phenotypes of mutants in which a retrotransposon was inserted in genomic sequences and for comprehensive gene function anal-
these hormone-responsive genes, we identified phenotypes related to ysis at transcriptional and translational levels. On the basis of
seed formation or plant height, including sterility, vivipary, and the results of our large-scale FL-cDNA analysis (18), we have
dwarfism. In comparison of cis-elements for hormone response genes
between rice and Arabidopsis thaliana, we identified cis-elements for
constructed a monitoring system that uses an oligonucleotide
dehydration-stress response as Arabidopsis specific and for protein array to monitor gene transcriptional levels and to develop
storage as rice specific. genome-wide functional analysis of rice. The array was com-
posed of 21,938 probes with 60-mer oligonucleotides synthe-
sized at a gene-specific region (2, 13, 34) from 32,127 FL-
Article published online before print. See web site for date of publication cDNAs. Mapping of these cDNA clones to genomic DNA
(http://physiolgenomics.physiology.org).
Address for reprint requests and other correspondence: S. Kikuchi, National
revealed that there are about 20,500 transcriptional units (TUs),
Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki and clustering of these cDNA clones revealed a unique clone
305-8602, Japan (E-mail: skikuchi@nias.affrc.go.jp). set. Of the ⬃20,500 TUs located on genomic DNA, single
1094-8341/04 $5.00 Copyright © 2004 the American Physiological Society 87
88 PROFILING OF PHYTOHORMONE-RESPONSIVE GENES IN RICE
clones on TU are ⬃14,000 and multiple clones on TU are Plant Material and RNA Preparation
⬃16,000 (⬃6,500 TUs). About 2,000 clones were unmapped The callus used for total RNA extraction was derived from the
according to incomplete genome sequences. The probes were scutellum of the japonica rice cultivar “Nipponbare” and was culti-
selected from these results. vated in Murashige and Skoog medium (27) containing 10 M
We used the arrays as probes to hybridize target RNAs 2,4-dichlorophenoxyacetic acid. Such callus maintains the ability to
prepared from normally grown callus and from callus treated develop roots and leaves. After the calluses had been cultured in the
with abscisic acid (ABA) or gibberellin (GA). The interaction medium for 30 days, they were transferred to a medium containing the
between ABA and GA is an important factor controlling the plant hormones ABA or GA and cultured for 3 days. The concentra-
transition from embryogenesis to germination in seeds. The tion of each plant hormone was adjusted to 50 M. After culturing,
effects of these hormones are competitive, in that ABA pro- we used an RNeasy Plant Mini Kit (Qiagen, Tokyo, Japan) to extract
total RNA from the hormone-treated calluses and from the control
motes seed dormancy, whereas GA promotes seed germina-
calluses (which were not treated with either hormone for the 3-day
tion. Cereals are excellent plants in which to explore the period). mRNA was isolated with an Oligotex-dt30 (Super) mRNA
molecular mechanisms involved in hormonally regulated gene purification kit (Takara, Shiga, Japan). Purified mRNA was amplified,
expression, particularly the antagonism between ABA and GA labeled, and hybridized to the rice 22,000-oligonucleotide array ac-
(14). Reports of such explorations (10, 22) have suggested the cording to the manufacturer’s protocols (Agilent Technologies). For
presence of cross talk, but these studies have investigated only each experiment described in this study, the data presented represent
We compared ABA response genes in plants among our OsDREB1B (AK062422; a drought-inducible gene) and a gene
result and other results of comprehensive expression analysis homolog for osmotic-inducible ankyrin kinase (AK100268),
(12, 29, 33) using MIPS code and accession ID (Table 1). were upregulated by GA treatment (“stress” category in Sup-
Among them, 200 (this report), 1,401 (12), 43 (29), and 493 plemental Table S2). Such genes had not previously been
(33) genes are candidates for ABA-inducible genes, respec- reported as GA responsive, except for metallothionein-related
tively. These inconsistencies of genes among these results may gene homologs (AK062653, AK103445) (38). Some of the
be attributed to the biological differences among plant species downregulated genes included had already been functionally
used, organ/tissues, ABA treatment condition, their response to annotated as responsive to GA (38) (“hormone, GA” and
ABA, and/or detection methodology. “storage protein” categories in Supplemental Table S2). These
genes included homologs of genes for hydrophobic LEA-like
Genes with Altered Expression Levels in Callus Cultured protein (AK102039) and RAB24 (AK102982), which was
with GA for 3 days reported as not only GA inducible but also antagonistically
ABA inducible (upregulated) (38). Eight genes related to
The SD of the [log2(average ratio)] of four replications of development had not previously been reported as GA respon-
the experiment was 0.311 after removal of flagged data, and all sive (“development” category in Supplemental Table S2). The
the selected genes in Supplemental Table S2 were contained in gene homolog for calcium-binding protein, CaBP1, in barley
the area of the median (0.00) ⫾3SD over a normal distribution.
Upregulated
J033072B12 AK073858 3.3 NADP-malic enzyme (Aloe arborescens) Development At2g19900 Malate oxidoreductase 2.4 3.2 4.4 9.3 5.3
(malic enzyme)
J023101G03 AK071637 3.2 Protein phosphatase 2C Development At5g24940 Protein phosphatase BP432943 AK071637
(Mesembryanthemum crystallinum) 2C-like protein
006-210-H01 AK061224 2.5 Raffinose synthase, Rfs (Cucumis sativus) Development At5g40390 Glycosyl hydrolase 5.2 2.5 1.5 1.3 1.9
family 36
J023078G01 AK100306 1.9 Sucrose synthase type 2 (Triticum Development At3g43190 Sucrose synthase-like ⫺4.4
aestivum) protein
002-169-E03 AK110652 9.4 Glucose and ribitol dehydrogenase Hormone, At1g54870 Dormancy related 1.4 1.6 1.9 1.7 2.6
homolog (Hordeum vulgare) ABA protein, putative
001-117-H05 AK063578 2.8 ABA-responsive protein (H. vulgare) Hormone, At5g13200 ABA-responsive 4.1 BP432968 AK063578
ABA protein-like
001-124-F05 AK105433 2.3 Heat shock protein, HSP101 (Oryza Stress At1g74310 Heat shock protein 101 3.0
sativa) (HSP101)
001-119-F01 AK063685 2.9 Homeodomain leucine zipper protein, Transcriptional At2g46680 Homeodomain 6.8 7.5 8.8 18.8 13.9 27.7
Oshox6 (O. sativa) factor transcription factor
(ATHB-7)
001-118-H06 AK063645 6.6 Unknown Unclassified At1g01470 Hypothetical protein 5.8 7.2 4.0 5.1 2.7 4.6
002-140-G05 AK108233 6.1 Unknown Unclassified At2g22170 Unknown protein ⫺5.8
17 •
factor X2 (O. sativa)
J023012K18 AK069274 4.1 Unknown Unclassified At1g07430 Protein phosphatase 2C 115.0
(PP2C)
002-169-F02 AK110661 3.5 Unknown Unclassified At1g03790 Unknown protein 25.0
containing CCCH-
type zinc finger
J013146J07 AK068272 2.9 Unknown Unclassified At5g59220 Protein phosphatase 2C 36.6
(PP2C)
002-175-E10 AK111075 2.8 Unknown Unclassified At1g27300 Hypothetical protein 3.1
J023037K22 AK069960 2.7 Unknown Unclassified At5g54160 O-methyltransferase 1 BP433009 AK064768
www.physiolgenomics.org
001-120-E03 AK063729 2.7 Unknown Unclassified At3g18280 Lipid transfer protein, 1.0 1.2 1.5 2.5 3.4
putative
002-124-C12 AK107138 2.2 Unknown Unclassified At5g14180 Putative protein 1.6 2.7 3.9 7.1 6.4 ⫺6.8
PROFILING OF PHYTOHORMONE-RESPONSIVE GENES IN RICE
Downregulated
002-114-G10 AK106723 0.4 ␣-Amylase/subtilisin inhibitor, BASI (H. Hormone, At1g73260 Putative trypsin 1.5 2.4 9.7 11.9 7.0 3.7
vulgare) ABA inhibitor
002-108-G04 AK064395 0.5 IAA (anxin indole-3-acetic acid)-glu Hormone, At2g43820 Putative 1.0 1.8 2.1 3.1 3.3
synthetase, iaglu (Zea mays) others glucosyltransferase
J033052E11 AK073667 0.4 OsNAC3 protein (O. sativa) Transcriptional At1g77450 GRAB1-like protein 18.1
factor
002-111-B07 AK064485 0.4 Unknown Unclassified At3g02040 Hypothetical protein 3.1
001-123-G04 AK063959 0.3 Unknown Unclassified At2g38290 Ammonium transporter 17.0
AtAMT2
MIPS Code indicates gene identification of the sequence in the Munich Information Center for Protein Sequences (MIPS). *cDNA microarray data for a set of transcripts previously reported as ABA
responsive (33) and modified here were compared with our expression data. †Expression profile of ABA-responsive gene previously reported (12) and modified here was compared with our data. ‡cDNA
microarray data for a set of transcripts previously reported as ABA responsive (29) and modified here were compared with our data. Details of all experimental conditions refer to each report (12, 29, 33).
See legend to Supplemental Table S1 for explanation of other column names. ABA, abscisic acid; FL-cDNA, full-length complementary DNA; EST, expressed sequence tag.
91
almost the same level (average ratio ⫽ 1.0384) in GA-treated defense-related genes and gene homologs by ABA and GA
and untreated callus. (See deposited data, GSE661 including treatment suggests that the plant seed does not require high
GSM9857 through GSM9860, at the NCBI GEO database.) levels of protection from threats such as pathogens in the
The gene homolog (AK063685) for the homeodomain leucine external environment, but that at germination the plant is more
zipper protein family, which has a role as a developmental vulnerable and the defense-related genes are therefore upregu-
regulator, was newly found to be downregulated by GA. We lated. The fact that a gene for MADS-box-like protein
found 132 genes with unknown functions that were upregu- (AK111859), which functions in the construction of the repro-
lated by GA treatment and 66 that were downregulated. These ductive organs (30), was regulated antagonistically by ABA
unknown genes were newly classified as GA responsive. and GA suggests that the gene might have a new function
We performed a comprehensive analysis of gene expression related to seed dormancy and germination. Forty-two clones of
using callus tissue treated with ABA or GA. Genes for em- genes with unknown functions were newly assigned functions
bryogenesis, germination, seed dormancy, and grain filling as genes antagonistically responsive to ABA and GA treat-
were included among those with altered expression levels. The ment. Fifteen genes were reported as representing genes re-
fact that the experiments identified many already known ABA- sponsive to both hormones in our previous study, which used
and GA-responsive genes in other tissues shows that callus the rice 8,987-cDNA microarray and quantitative RT-PCR
tissue can be mimic the mechanisms of germination and (38). In contrast, we detected 66 genes responsive to both
A: Comparison of cis-element numbers among genes upregulated by ABA, downregulated by GA, and both upregulated by ABA and downregulated by GA
Upregulated by ABA, downregulated by GA Development MYBPZM
Light IBOX, BOXIIPCCHS
Other hormone CATATGGMSAUR, MARTBOX
Protein storage RYREPEATVFLEB4, ACGTABREMOTIFA2OSEM,
DPBFCOREDCDC3, CACGTGMOTIF,
RYREPEATLEGUMINBOX, TATABOX3,
RYREPEATGMGY2
Downregulated by GA Defense SEBFCONSSTPR10A
Development ACGTCBOX
Light TBOXATGAPB
Other hormone ERELEE4
Stress (dehydration) MYCATRD22
Upregulated by ABA Light TBOXATGAPB
Storage protein RAV1BAT, CANBNNAPA
upstream regions of genes that were both upregulated by GA external environment during germination, or that germination
and downregulated by ABA. Genes downregulated by ABA is in fact a phenomenon of self-stress. In addition, these results
and genes upregulated by GA were rich in cis-elements for suggest that plant cells are resistant to receive stress from the
stress response (MYBPLANT, TATABOXOSPAL, upregu- external environment during seed dormancy. We compared the
lated by GA; LTRECOREATCOR15, PALBOXAPC, down- cis-elements for tissue-specific response between parts A and B
regulated by ABA) in the upstream regions. Cis-element for of Table 2. There are nine kinds of cis-element for seed protein
the defense response (SEBFCONSSTPR10A) was specified as storage in Table 2A. Seven kinds of element for protein storage
an element common to both the gene group upregulated by GA were included in the gene group both upregulated by ABA and
and the group downregulated by ABA. These results suggest downregulated by GA, demonstrating that this group is related
that antagonistic-response genes regulated by ABA treatment to seed dormancy. In contrast, two elements (AMYBOX1,
(Table 2A) or GA treatment (Table 2B) have cis-elements such TATCCAOSAMY) for seed germination response were in-
as RYREPEATVFLEB4 (“protein storage” category in Table cluded in the gene group both upregulated by GA and down-
2A) and AMYBOX1 (“amylase” category in Table 2B), which regulated by ABA (Table 2B) and were thus related to seed
are related to seed dormancy and germination, respectively. In
germination. The variety of cis-elements for protein storage in
contrast, genes for response to only one of the two hormones
the gene group both upregulated by ABA and downregulated
are rich in elements such as MYCATRD22 [“stress (dehydra-
by GA (Table 2A), which mimics seed dormancy, is larger than
tion)” category in Table 2A] and SEBFCONSSTPR10A (“de-
fense” category in Table 2B), which promote seed dormancy those for amylase in the gene group both upregulated by GA
and germination, respectively. and downregulated by ABA (Table 2B), which mimics germi-
Cis-elements for stress response were richer in the gene nation. We do not know whether the cis-elements of the latter
groups of Table 2B than those of Table 2A. There are five group have multiple functions or whether they are poorly
elements for stress-response factor (MYBST1, MYBPLANT, represented on the PLACE database.
TATABOXOSPAL, LTRECOREATCOR15, and PALBOX- In promoter sequences search of the ABA response genes
APC) in Table 2B. MYBST1, for responding to various obtained, we detected that several genes (AK064966,
stresses, was included in the gene group both upregulated by AK073100, AK073380, AK073777, AK073833, AK102307,
GA and downregulated by ABA, which demonstrates that it is AK103170, AK105316, AK106508, AK108159, AK110259,
related to stress response in seed germination. In contrast, one and AK110912 in Supplemental Table S4) did not contain any
element for dehydration stress response (MYCATRD22) was ABA-responsive element in their promoters as well as other
rich in genes upregulated by ABA and genes downregulated by report (29). These results suggest the existence of novel cis-
GA (“stress” category in Table 2A). We speculate that plant acting elements involved in ABA-inducible gene expression in
cells are particularly susceptible to receive stress from the their promoters.
Physiol Genomics • VOL 17 • www.physiolgenomics.org
94 PROFILING OF PHYTOHORMONE-RESPONSIVE GENES IN RICE
Phenotypes of Transposon Insertion Mutants in legumes at the onset of germination and during the early
stage of nodule development (3). The phenotypes of dwarfism,
To elucidate the functions of the genes responsive to our brittleness, and lethality indicate growth delay and suggest that
treatments, we investigated the phenotypes of mutants in which
disruption of this gene led to reduced protein synthesis for
the rice retrotransposon Tos17 was inserted in the regions of
plant growth using nitrogen because of disruption of nitrogen
these responsive genes with the aid of a Tos17 mutant panel
metabolism pathways. Because, unlike legumes, rice does not
database (http://tos.nias.affrc.go.jp/). Tos17, which is highly
activated by tissue culture, has been used for insertion mu- form root nodules, we speculate that this gene homolog may
tagenesis of rice (24). The Tos17 mutant panel database en- play a role in nitrogen metabolism with regard to plant growth
ables one to link flanking sequences with phenotype informa- dependent on ABA and GA signal transduction. The phenotype
tion by using the BLAST program. With this database, one can of the insertion mutant of the gene homolog for protein
perform gene function analysis by computer and reverse ge- phosphatase (AK068272) of Lotus japonicus, which has a
netics. We obtained 12 insertion mutants from the 200 ABA- function in nodules that are in the process of initiating nitrogen
responsive genes (Table 3). Gene homologs for ankyrin kinase fixation (16), showed sterility. Loss of function of the gene
(AK100268), protein phosphatase type 2C (AK068272), and homolog in response to Tos17 insertion might reduce protein
zinc transporter protein (AK105258) had functional annota- storage during seed formation by disruption of a nitrogen
tions in a BLASTX search on NCBI (identities ⬎40%) and in metabolism pathway. We speculate that the gene homolog may
Table 3. Results of a phenotype search of insertion mutants of ABA-responsive genes, using Tos17
BLASTN BLASTX
Average
Clone Name Accession No. Ratio Tos17 ID Phenotype Putative Gene ID Accession No. Putative Gene ID Accession No.
002-112-G01 AK064587 4.82 NC2670_0_404_1A No comment Clone 26360 AY086623.1 Putative eukaryotic peptide AY034963.1
(Arabidopsis chain release factor
thaliana) subunit 1 (A. thaliana)
002-112-G01 AK064587 4.82 H0732_1_102_1A Dwarf Clone 26360 AY086623.1 Putative eukaryotic peptide AY034963.1
(A. thaliana) chain release factor
subunit 1 (A. thaliana)
J033082H02 AK102075 3.14 NE8550_0_105_1A Dwarf Unknown AT5g23390/T32G24_2 AY090230.1
mRNA (A. thaliana)
J013146J07 AK068272 2.91 T09854T Sterility Unknown Nodule-enhanced protein AF092431.1
phosphatase type 2C,
NPP2C1 (Lotus
japonicus)
002-105-E08 AK064271 2.59 T14722T Sterility Unknown Heat stress transcription X67601.1
factor 30, Lp-hsf30
(Lycopersicon
peruvianum)
001-114-G07 AK105258 2.35 ND5061_0_103_1A No comment Unknown Zinc transporter protein, AY029321.1
ZIP1 (Glycine max)
001-114-G07 AK105258 2.35 NE1520_0_101_1A White-based Unknown Zinc transporter protein, AY029321.1
rice kernel ZIP1 (G. max)
006-303-C01 AK109407 0.47 NC0021_0_702_1A Viviparous, Unknown AT3g48690/T8P19_200 AY064980.1
Dwarf, mRNA (A. thaliana)
Chlorina
002-173-G04 AK110936 0.39 NF5045_0_405_1A Growth delay, Unknown Benzoic acid carboxyl AF198492.1
Zebra leaf, methyltransferase,
Dwarf BAMT (Antirrhinum
majus)
J023065A22 AK100268 0.36 NC0584_0_403_1A No comment Ankyrin-kinase AF458699.1 Ankyrin-kinase (M. AF458699.1
(Medicago truncatula)
truncatula)
J023065A22 AK100268 0.36 T01783T Dwarf, Brittle Ankyrin-kinase AF458699.1 Ankyrin-kinase (M. AF458699.1
(M. truncatula) truncatula)
J023065A22 AK100268 0.36 T12791T Lethal, Dwarf, Ankyrin-kinase AF458699.1 Ankyrin-kinase (M. AF458699.1
Low (M. truncatula) truncatula)
germination
rate
“Tos17 ID” indicates the original identification number of the flanking sequence submitted to the Rice Tos17 Insertion Mutant Database. “Phenotype” indicates the
original comment on the picture of the mutant submitted to the Rice Tos17 Insertion Mutant Database. See caption to Supplemental Table S1 for explanation of other
column names.
Table 4. Results of a phenotype search of insertion mutants of GA-responsive genes, using Tos17
BLASTN BLASTX
Accession Accession Accession
Clone Name No. Average Ratio Tos17 ID Phenotype Putative Gene ID No. Putative Gene ID No.
001-019-H08 AK058750 0.35 NC0238_0_407_1A No comment myo-Inositol AB012107.1 myo-Inositol phosphate synthase, AB012107.1
phosphate RINO1 (O. sativa)
synthase, RINO1
(Oryza sativa)
001-113-C06 AK063277 2.24 NF3020_0_104_1A No comment Unknown Unknown
001-200-B09 AK105614 2.64 NF4021_0_401_1A No comment Unknown PV72 (Cucurbita cv. Kurokawa AB006809.1
Amakuri)
002-112-E08 AK064577 0.37 T24162T No comment Unknown Unknown
002-112-E08 AK064577 0.37 T08819T Vivipary Unknown Unknown
J013000A05 AK064768 2.71 T11716T Dwarf Caffeic acid 3-O- AJ231133.1 Caffeic acid O-methyltransferase AF153825.1
methyltransferase (Festuca arundinacea)
(Saccharum
officinarum)
J013099F12 AK067444 2.62 T11806T Albino Cell wall invertase, AF030421.1 Cell wall invertase, IVR3 (T. AF030421.1
IVR3 (Triticum aestivum)
common elements that were present in at least one gene in both exist in rice. However, the number of cis-elements for
species. protein storage was remarkably rich in both species (“com-
Six kinds of cis-elements for dehydration-stress re- mon” in “specific or common” column in Table 5), and the
sponse (ACGTATERD1, MYB1AT, ABRELATERD1, number of other elements for protein storage (⫺300ELE-
MYB2CONSENSUSAT, MYCATERD1, MYCCONSEN- MENT, RYREPEATGMGY2, RYREPEATLEGUMIN-
SUSAT) were specified as elements in Arabidopsis (italic BOX, RYREPEATBNNAPA) were richer in the upstream
characters in “cis-element” column in Table 5). The speci- regions of genes of rice than in those of Arabidopsis. We
ficities of Arabidopsis cis-elements for dehydration stress suggest that Arabidopsis might use these conserved ele-
might be derived from differences in the growth environ- ments for protein storage. The specificities of rice in protein
ments of each species. These six kinds of elements do not storage might be derived so that structure of rice seed is
Physiol Genomics • VOL 17 • www.physiolgenomics.org
98 PROFILING OF PHYTOHORMONE-RESPONSIVE GENES IN RICE
Table 6. Comparison of cDNA array, 60-mer oligo array and Q-RT-PCR relative expression results
for ABA responsive transcripts
Q-RT-
cDNA Array 60-mer Oligo Array PCR
Category Putative gene ID Clone Name Accession No. Ratio Oligo Array Ratio Ratio
Cell growth Aldose-reductase-related protein (Avena fatua) CH2836 AU101007 4.47 J013074I15 8.21 9.99
Cell growth Glucose dehydrogenase (Hordeum vulgare) EC0269 C19333 4.56 002-169-E03 9.39 19.40
Cell growth Lipid transfer protein (Oryza sativa) CH3458 AU063655 2.17 J033094A19 1.03
Cell growth Lipid transfer protein (O. sativa) ST3943 D41439 2.17 006-205-A04 0.93 6.12
Cell growth Mitochondrial phosphate transporter (O. sativa) EC0376 C99183 2.84 J023022H13 0.84 4.9
Cell growth myo-inositol phosphate synthase, RINO1 (O. sativa) CH0155 C97424 2.41 001-019-H08 2.08 7.77
Cell growth myo-inositol phosphate synthase, RINO1 (O. sativa) CB2444 AU068211 2.37 001-019-H08 2.08 1.00
Cell growth myo-inositol phosphate synthase, RINO1 (O. sativa) FE0401 AU174807 2.16 001-019-H08 2.08 5.86
Cell growth Proteinase inhibitor, RPI (O. sativa) EC1619 AU172733 7.14 002-125-A10 1.02 93.11
Defense 16 kDa oleosin, ole16 (O. sativa) EC0540 C19519 3.01 J03317E10 1.60
Defense 16 kDa oleosin, ole16 (O. sativa) EC1755 C20257 2.45 J033127E10 1.60 18.02
Defense Hydrophobic LEA-like protein (O. sativa) CH2085 C28696 3.64 001-118-B01 4.76 5.71
different from that of Arabidopsis. Also, that the cis-element all types of cis-elements of GA-responsive genes in rice and
for expression of the amylase gene (CGACGOSAMY3) was Arabidopsis are shown in Supplemental Tables S8 (rice) and
specified as an element in rice may suggest the view that the S9 (Arabidopsis). The results of comparison between 151
difference in these elements is derived from differences in clones responsive to GA in rice and 117 clones of corre-
organization between rice and Arabidopsis. Although the sponding Arabidopsis genes are summarized in Supplemen-
cis-element MYBCORE for water-stress response appears in tal Table S10. The comparison of cis-elements for GA-
both species as a common cis-element in Table 5, the responsive genes between rice and Arabidopsis gives a
number of elements in rice was 1.34 times that in Arabi- result similar to that for ABA. These differences in cis-
dopsis. These results suggest that rice might use a slightly elements for protein storage and dehydration-stress response
different mechanism for response to water stress. Two kinds between rice and Arabidopsis may have accumulated
of ABA-responsive element (RAV1AAT, DPBFCORED- through differences in the organization of each plant or
CDC3) and one GA-responsive element (DOFCOREZM) through evolutionary responses to the growth environment.
were rich in cis-elements conserved between rice and Ara- The comparative analysis of cis-elements among various
bidopsis (“common” in “specific or common” column in species for the detection of characteristic in plants may
Table 5). We suggest that each species might have a com- become a useful indicator for the more efficient creation
mon pathway for ABA or GA metabolism. The numbers of of transgenic plants. The comparison also may support the
Physiol Genomics • VOL 17 • www.physiolgenomics.org
PROFILING OF PHYTOHORMONE-RESPONSIVE GENES IN RICE 99
prediction of the physiological functions of the products ABA and GA response in rice. We identified genes that had
of “unknown” genes. In promoter sequences search of never before been annotated as ABA or GA responsive in other
the ABA response genes obtained, we detected that several reports of comprehensive expression analysis of ABA-respon-
rice genes (AK064966, AK073100, AK073380, AK073777, sive genes in plant (12, 29, 33), detected new interactions
AK073833, AK102307, AK103170, AK105316, AK106508, between genes responsive to the two hormones, comprehen-
AK108159, AK110259, and AK110912 in Supplemental Table sively characterized cis-elements of hormone-responsive
S6) did not contain any ABA-responsive element in their genes, obtained new putative gene functions from phenotypic
promoters on rice genome as well as Arabidopsis report (33). results, and characterized cis-elements of rice and Arabidopsis.
These results suggest the existence of novel cis-acting elements The results revealed that our tools and methods of functional
involved in ABA-inducible gene expression in their promoters genomics can identify genes that control particular phenotypes
of rice and Arabidopsis. In our study, WRKY transcription and can identify the transcriptional regulator (cis-element) of
factor (AK073100, AK110912 in Supplemental Table S6), a rice faster and more accurately than ever before. For the most
protein known to mediate the pathogen-induced defense pro- effective functional analysis of the genome, all available in-
gram, were induced by ABA treatment in rice callus. The data formation needs to be integrated. Systematically connecting
suggest that these not only reveal the cross talk between ABA powerful tools and information for functional genomics of rice
response pathway and pathogen-induced defense program but will allow researchers in the life sciences, especially crop
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