11105_2011_364_MOESM3_ESM

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11105_2011_364_MOESM3_ESM
Strand
No of
element
Sequence of element
Characterization
Description
Reference
-1010
(-)
RSP00024
TATTATTT
P. sativum /GENE: petE /RE: A/T- rich BOX3 /BF: PCF1
petE = Pea plastocyanin gene
(Helliwell et al. 1997), (Sullivan
and Gray 2002)
-975
(-)
RSP00026
gcttttgaTGACtTcaaacac
-1009
(-)
RSP00026
N. tabacum /GENE: G13 /RE: -141 sequence /BF: TGA1a;
PG13;
G13 = Leucine zipper DNA binding protein related to the TGA1a
(Fromm et al. 1991)
-1104
(+)
RSP00098
-1038
(-)
RSP00098
gcttttgaTGACtTcaaacac
cttaatatATTTTTAattattttatt
ctcttaa
cttaatatATTTTTAattattttatt
ctcttaa
P. sativum /GENE: rbcS-3.6 /RE: AT-1 /BF: AT-1
rbcS = ribulose-1,5-bisphosphate carboxylase - oxygenase gene
-1012
(+)
RSP00102
aaaTGACGaaaatgc
C. sativus /GENE: hpr-A /RE: as-1 LM /BF: unknown nuclear
factor
hrp-A= hydroxypyruvate reductase gene / as-1 = activation sequence-1like element
(Gilmartin et al. 1990)
(Schwartz et al. 1991),
(Garreton et al. 2002), (Lam et
al. 1989)
-1100
(+)
RSP00117
aattATTTTTAaa
-1042
(-)
RSP00117
aattATTTTTAaa
N. plumbaginifolia /GENE: cab-E/RE: AT-1 (2) /BF:
unknown nuclear factor
Cab-E = photoregulated CAB gene (Cab-E) (CAB polypeptides bind
chlorophyll a and b)
(Castresana et al. 1988)
-1099
(+)
RSP00125
aatATTTTTAtt
-1043
(-)
RSP00125
-1108
(+)
RSP00126
-1034
(-)
RSP00126
aatATTTTTAtt
gaaaattttaatATTTTTAtttagt
att
gaaaattttaatATTTTTAtttagt
att
-1099
(+)
RSP00135
aatATTTTTAtc
-1043
(-)
RSP00135
aatATTTTTAtc
-1100
(+)
RSP00140
aattATTTTTAtt
-1042
(-)
RSP00140
aattATTTTTAtt
-958
(+)
RSP00161
WAAAG
-1037
(-)
RSP00161
WAAAG
Pos.
-1135
(-)
RSP00161
WAAAG
-1103
(-)
RSP00252
-1024
(+)
RSP00269
CACATG
atcttatgtcattgaTGACGacctc
c
-1112
(+)
RSP00282
TATCCAT
-957
(-)
RSP00282
TATCCAT
-967
(+)
RSP00308
CAACA
-1195
(+)
RSP00339
RTTTTTR
-1096
(+)
RSP00339
RTTTTTR
-1046
(-)
RSP00339
RTTTTTR
N. plumbaginifolia /GENE: cab-E/RE: AT-1 (3) /BF:
unknown nuclear factor
(Castresana et al. 1988)
L. esculentum /GENE: rbcS-3A/RE: AT-1 (1) /BF: unknown
nuclear factor
(Castresana et al. 1988)
N. plumbaginifolia /GENE: cab-E/RE: AT-1 (4) /BF:
unknown nuclear factor
(Castresana et al. 1988)
P. sativum /GENE: rbcS-3.6 /RE: AT-1 (2) /BF: AT-1
(Castresana et al. 1988)
Z. mays/ GENE: Synthetic oligonucleotids/RE: Dof1 BSopt
/BF: Dof1
A. thaliana/ GENE: rd22/RE: ATMYC BS / BF: rd22BP1
(MYC)
A. thaliana/GENE: GST6/RE: OBF5 BS /BF: OBF5
O. sativa /GENE: Amy3D/RE: Amylase-element /BF:
unknown nuclear factor
A. thaliana/GENE: synthetic oligonucleotides/RE: RAV1a
/BF: RAV1
rd22 = dehydration-responsive gene
gst6 = glutathione-S-transferase gene / ocs element binding factor
(OBF)
Amy3D = amylase-3D gene
RAV1 = Related to ABI3/VP1 proteins
(Yanagisawa and Schmidt
1999), (Yanagisawa 1997),
(Yanagisawa and Sheen 1998)
(Abe et al. 1997), (Abe et al.
1997)
(Chen et al. 1996), (Singh et al.
2002)
(Hwang et al. 1998)
(Kagaya et al. 1999), (Yamasaki
et al. 2004)
G. max/GENE: beta-conglicinin alfa'/RE: SEF4 BScons /BF:
SEF4
beta-conglicinin = seed-storage proteins in soybean / SEF: soybean
embryo factors
-1159
(-)
RSP00339
RTTTTTR
-1015
(-)
RSP00378
TTTGACT
-1001
(-)
RSP00404
TTTGCGT
-1016
(-)
RSP00436
TTGACT
-969
(-)
RSP00439
ATATTCTT
P. crispum/GENE: WRKY1/RE: WB /BF: WRKY1
N. tabacum/GENE: RNP2/RE: adja /BF: unknown nuclear
factor
A. thaliana/GENE: PR-1/RE: Zf-box /BF: unknown nuclear
factor
A. thaliana/GENE: PR-1/RE: -624-box /BF: unknown
nuclear factor
-900
(+)
RSP00463
atttcatggCCGACctgcttttt
A. thaliana/GENE: COR15a/RE: C-repeat/DRE /BF: CBF1
COR = cold-regulated genes
-900
(+)
RSP00464
acttgatggCCGACctctttttt
A. thaliana/GENE: COR15b/RE: C-repeat/DRE /BF: CBF1
COR = cold-regulated genes
-900
(+)
RSP00465
aatatactaCCGACcatgagttct
A. thaliana/GENE: COR78-1/RE: C-repeat/DRE /BF: CBF1
COR = cold-regulated genes
-1122
(+)
RSP00477
TTTAA
-1068
(+)
RSP00477
TTTAA
-1039
(+)
RSP00477
TTTAA
-1034
(-)
RSP00477
TTTAA
-1049
(-)
RSP00477
TTTAA
-1063
(-)
RSP00477
TTTAA
H. vulgare, B. napus /GENE: rbcSF1/RE: S-box /BF:
unknown nuclear factor
rbcS = ribulose 1,5-bisphosphate carboxylase gene
-1190
(+)
RSP00502
TACGTA
-1185
(-)
RSP00502
TACGTA
-1197
(+)
RSP00508
gcaTTTTTatca
-1141
(+)
RSP00508
gcaTTTTTatca
-1098
(+)
RSP00508
gcaTTTTTatca
-1044
(-)
RSP00508
gcaTTTTTatca
-1157
(-)
RSP00508
gcaTTTTTatca
-1112
(+)
RSP00511
TATCCATggtacatacggc
-957
(-)
RSP00511
TATCCATggtacatacggc
-944
(-)
RSP00565
GTATTTT
-1157
(-)
RSP00565
GTATTTT
-990
(+)
RSP00572
-1149
(+)
RSP00625
-1189
(-)
RSP00625
ATATGTCA
aaggtgatcatagagcaTATTAT
Aagagagtgaaaactaatgg
aaggtgatcatagagcaTATTAT
Aagagagtgaaaactaatgg
-1193
(-)
RSP00628
AACAATCT
(Yoshino et al. 2006), (Fujiwara
and Beachy 1994)
(Turck et al. 2004)
RNP2 = ribonucleoprotein
PR-1 = pathogenesis-related gene
(Rushton et al. 1996), (Lebel et
al. 1998)
(Rushton et al. 1996), (Lebel et
al. 1998)
(Jaglo-Ottosen et al. 1998)
(Nantel et al. 1991),
O. sativa/GENE: rifa-7-P-glucuronidase transgene/RE: Abox /BF: Different bZIP factors, including RITA-1
(Izawa et al. 1994)
G. max/GENE: beta-conglicinin alfa'/RE: SEF4 BS /BF: SEF4
(Yoshino et al. 2006), (Fujiwara
and Beachy 1994)
A. fatua/GENE: alpha-Amy2/A/RE: "TATCCAT" /BF:
unknown nuclear factor
(Willmott et al. 1998)
L. esculentum /GENE: rbcS3B/RE: AT-rich G /BF: unknown
nuclear factor
L. esculentum /GENE: rbcS1/RE: 3'/AT-rich J1 /BF:
unknown nuclear factor
G. max/GENE: GmAux28 /RE: A1 /BF: unknown nuclear
factor
A. thaliana/GENE: Lhcb1*3/RE: CCA1 BS1 /BF: CCA1
rbcS = ribulose 1,5-bisphosphate carboxylase gene
(Carrasco et al. 1993))
rbcS = ribulose 1,5-bisphosphate carboxylase gene
(Manzara et al. 1993)
Aux28 = auxin-responsive gene
Lhcb1*3 = light-harvesting Chl a/b proteins of PSII (formerly called cab
genes) / CCA1 = CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)
(Nagao et al. 1993)
(Andronis et al. 2008)
Supplementary References
Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and
MYB Homologs in Drought-and Abscisic Acid-Regulated Gene Expression. Plant Cell 9:1859-1868
Andronis C, Barak S, Knowles SM, Sugano S, Tobin EM (2008) The Clock Protein CCA1 and the bZIP Transcription
Factor HY5 Physically Interact to Regulate Gene Expression in Arabidopsis. Mol Plant 1:58-67
Carrasco P, Manzara T, Gruissem W (1993) Developmental and organ-specific changes in DNA-protein interactions
in the tomato rbcS3B and rbcS3C promoter regions. Plant Mol Biol 21:1-15
Castresana C, Garcia-Luque I, Alonso E, Malik VS, Cashmore AR (1988) Both positive and negative regulatory
elements mediate expression of a photoregulated CAB gene from Nicotiana plumbaginifolia. EMBO J 7:1929-1936
Chen W, Chao G, Singh KB (1996) The promoter of a H2O2-inducible, Arabidopsis glutathione S-transferase gene
contains closely linked OBF- and OBP1-binding sites. Plant J 10:955-966
Fromm H, Katagiri F, Chua N-H (1991) The tobacco transcription activator TGA1a binds to a sequence in the 5′
upstream region of a gene encoding a TGA1a-related protein. MGG 229:181-188
Fujiwara T, Beachy RN (1994) Tissue-specific and temporal regulation of a β-conglycinin gene: roles of the RY
repeat and other cis-acting elements. Plant Mol Biol 24:261-272
Garreton V, Carpinelli J, Jordana X, Holuigue L (2002) The as-1 Promoter Element Is an Oxidative Stress-Responsive
Element and Salicylic Acid Activates It via Oxidative Species. Plant Physiol 130:1516-1526
Gilmartin PM, Sarokin L, Memelink J, Chua N-H (1990) Molecular light switches for plant genes. Plant Cell 2:369378
Helliwell CA, Webster CI, Gray JC (1997) Light-regulated expression of the pea plastocyanin gene is mediated by
elements within the transcribed region of the gene. Plant J 12:499-506
Hwang YS, Karrer EE, Thomas BR, Chen L, Rodriguez RL (1998) Three cis-elements required for rice α-amylase
Amy3D expression during sugar starvation. Plant Mol Biol 36:331-341
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Highly Expressed during Seed Development. Plant Cell 6:1277-1287
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Overexpression Induces COR Genes and Enhances Freezing Tolerance. Science 280:104-106
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through two distinct DNA-binding domains uniquely found in higher plants. Nucl Acids Res 27:470-478
Lam E, Benfey PN, Gilmartin PM, Fang RX, Chua NH (1989) Site-specific mutations alter in vitro factor binding and
change promoter expression pattern in transgenic plants. Proc Natl Acad Sci USA 86:7890-7894
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controlling PR-1 gene expression in Arabidopsis. Plant J 16:223-233
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transgenic tobacco plants. Plant J 32:763-774
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WRKY1 to Its Native Promoter and the Defense-Related Gene PcPR1-1 in Parsley. Plant Cell 16:2573-2585
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B3 DNA Binding Domain of the Arabidopsis Cold-Responsive Transcription Factor RAV1. Plant Cell 16:3448-3459
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