Table I.
List of up-regulated ORGs
Up-regulated ORGs are shown. Microarray data for normalized fold expression are calculated from two biologically independent experiments. OPDA, JA, and MeJA were treated for plants grown in liquid culture, whereas wounding was performed for plants grown in solid medium. Normalized fold expression more than 3 is in bold. See also Supplemental Table I.
| Normalized Fold Expression
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|
| Annotation | Gene Name | OPDA
|
JA
|
MeJA
|
Wounding
|
||||
| 30 min | 180 min | 30 min | 180 min | 30 min | 180 min | 30 min | 180 min | ||
| Group 1: Signaling Component | |||||||||
| Phophatase | |||||||||
| Protein phosphatase 2C (PP2C), putative | At3g27140 | 3.0 | 1.5 | 1.4 | 1.3 | 0.9 | 0.5 | 1.6 | 0.4 |
| Protein kinase | |||||||||
| Protein kinase family (OXI1) | At3g25250 | 12.1 | 3.1 | 1.3 | 1.8 | 0.6 | 0.9 | 10.0 | 1.1 |
| Protein kinase family | At4g25390 | 1.9 | 3.5 | 1.0 | 1.5 | 1.1 | 1.8 | 2.2 | 2.2 |
| Protein kinase family (MAPKKK18) | At1g05100 | 3.7 | 3.0 | 1.1 | 1.1 | 1.0 | 1.6 | 5.7 | 2.6 |
| Protein kinase, putative | At2g05940 | 4.2 | 1.6 | 1.2 | 1.5 | 1.3 | 1.2 | 1.5 | 0.7 |
| Receptor-related protein kinase like | At5g25930 | 9.6 | 7.1 | 1.3 | 1.4 | 1.3 | 1.3 | 7.4 | 0.9 |
| Calcium-binding protein | |||||||||
| Calcium-binding EF-hand family protein | At4g27280 | 3.5 | 0.8 | 0.6 | 0.3 | 0.7 | 0.4 | 0.4 | 0.4 |
| Calcium-binding EF-hand family protein | At5g39670 | 6.0 | 2.8 | 1.1 | 0.8 | 1.4 | 0.8 | 1.5 | 1.1 |
| Calcium-binding protein, putative (PBP1) | At5g54490 | 3.7 | 0.7 | 0.5 | 0.5 | 0.5 | 0.4 | 1.0 | 0.4 |
| Calcium-transporting ATPase, putative | At3g63380 | 1.2 | 3.4 | 0.7 | 1.1 | 1.1 | 1.0 | 2.4 | 8.1 |
| Calmodulin-binding protein | At5g26920 | 4.4 | 0.9 | 1.0 | 0.6 | 0.8 | 0.7 | 1.1 | 0.3 |
| Calmodulin-related protein, putative | At3g01830 | 8.1 | 0.9 | 1.3 | 0.6 | 1.1 | 0.7 | 12.2 | 1.0 |
| Calmodulin-related protein, putative | At5g42380 | 5.5 | 5.0 | 1.1 | 0.7 | 1.2 | 0.8 | 6.3 | 1.3 |
| Other signaling component | |||||||||
| F-box protein family | At1g61340 | 4.4 | 0.9 | 1.0 | 0.6 | 1.1 | 0.7 | 6.9 | 1.2 |
| Transcription factor inhibitor I κ B like | At5g45110 | 3.4 | 1.4 | 1.4 | 1.0 | 1.1 | 0.9 | 2.2 | 0.7 |
| Response regulator 2 (ATRR2) | At3g48100 | 3.7 | 0.6 | 1.5 | 0.7 | 1.5 | 0.9 | 1.0 | 0.3 |
| SigA-binding protein (SIB1) | At3g56710 | 7.5 | 1.5 | 1.2 | 0.7 | 1.1 | 0.6 | 1.2 | 0.7 |
| Group 2: Transcription Factor | |||||||||
| AP2-EREB-type transcription factor | |||||||||
| AP2 domain transcription factor TINY, putative | At1g22810 | 13.9 | 1.5 | 1.3 | 1.2 | 1.5 | 1.1 | 58.8 | 5.2 |
| AP2 domain transcription factor, putative | At1g19210 | 6.1 | 1.2 | 1.0 | 1.0 | 1.1 | 1.2 | 1.3 | 0.3 |
| C-repeat/DRE-binding protein, putative | At5g52020 | 2.1 | 6.3 | 1.4 | 1.0 | 0.9 | 0.8 | 1.9 | 1.0 |
| DRE-binding protein (DREB2A) | At5g05410 | 7.3 | 4.4 | 0.7 | 0.9 | 1.6 | 1.9 | 7.9 | 2.8 |
| Ethylene responsive element binding factor 5 (AtERF5) | At5g47230 | 4.3 | 0.9 | 0.9 | 0.5 | 0.9 | 0.5 | 0.3 | 0.3 |
| Transcription factor TINY, putative | At1g33760 | 3.6 | 0.6 | 0.9 | 0.7 | 1.0 | 0.5 | 0.6 | 0.1 |
| WRKY-type transcription factor | |||||||||
| WRKY family transcription factor (WRKY30) | At5g24110 | 5.8 | 1.0 | 0.7 | 0.5 | 0.7 | 0.5 | 9.7 | 0.3 |
| WRKY family transcription factor (WRKY46) | At2g46400 | 3.7 | 0.7 | 1.0 | 0.6 | 1.1 | 0.8 | 1.3 | 0.5 |
| WRKY family transcription factor (WRKY53) | At4g23810 | 3.1 | 0.2 | 0.4 | 0.2 | 0.3 | 0.2 | 2.0 | 0.4 |
| MYB-type transcription factor | |||||||||
| Myb family transcription factor (MYB15) | At3g23250 | 5.1 | 1.5 | 1.8 | 1.5 | 1.5 | 1.2 | 34.6 | 4.5 |
| Transcription factor (MYB4) | At4g38620 | 5.6 | 0.9 | 0.7 | 1.1 | 0.7 | 0.8 | 1.0 | 0.9 |
| Zinc-finger-type transcription factor | |||||||||
| C2H2-type zinc-finger protein family | At2g28710 | 2.6 | 4.5 | 0.7 | 0.8 | 0.7 | 0.7 | 0.3 | 0.7 |
| C2H2-type zinc-finger protein related | At2g37430 | 10.2 | 1.1 | 1.4 | 1.5 | 1.0 | 1.0 | 4.5 | 0.7 |
| C2H2-type zinc-finger protein related (FZF) | At2g24500 | 1.2 | 3.1 | 0.9 | 1.1 | 0.9 | 1.4 | 2.0 | 4.7 |
| CONSTANS B-box zinc-finger family protein | At2g47890 | 2.2 | 3.1 | 1.0 | 1.0 | 0.9 | 0.9 | 1.3 | 1.5 |
| CONSTANS B-box zinc-finger family protein | At3g21150 | 3.3 | 1.0 | 0.9 | 0.7 | 0.8 | 1.2 | 1.4 | 0.5 |
| RING-H2 zinc-finger protein related | At5g27420 | 3.4 | 0.5 | 0.4 | 0.3 | 0.5 | 0.3 | 1.3 | 0.2 |
| Salt-tolerance zinc-finger protein (ZAT10) | At1g27730 | 7.0 | 1.7 | 1.2 | 0.7 | 1.3 | 0.7 | 1.6 | 0.7 |
| Zinc-finger protein (PMZ) | At3g28210 | 3.7 | 17.4 | 0.7 | 0.8 | 0.9 | 1.0 | 14.5 | 23.6 |
| Zinc-finger protein Zat12 (RHL41) | At5g59820 | 6.4 | 3.5 | 1.0 | 1.2 | 1.4 | 1.8 | 1.9 | 1.1 |
| Zinc-finger-related protein | At3g46080 | 5.1 | 1.7 | 0.9 | 0.7 | 0.8 | 1.0 | 2.9 | 1.7 |
| Other-type transcription factor | |||||||||
| bHLH protein family | At2g28160 | 4.0 | 3.7 | 1.7 | 1.5 | 1.0 | 1.4 | 1.5 | 1.1 |
| Transcription factor GT-3a | At5g01380 | 1.8 | 4.0 | 1.0 | 1.2 | 0.9 | 0.6 | 15.7 | 12.3 |
| Group 3: Stress Response | |||||||||
| Pathogenesis related | |||||||||
| Disease resistance protein (TIR class), putative | At2g20145 | 3.2 | 1.5 | 1.3 | 0.9 | 1.0 | 0.9 | 1.6 | 2.0 |
| Disease resistance protein (TIR-NBS class), putative | At1g66090 | 5.3 | 0.9 | 0.8 | 0.6 | 0.9 | 0.7 | 2.4 | 0.5 |
| Disease resistance protein family (LRR) | At3g05360 | 1.0 | 3.3 | 0.9 | 1.3 | 1.0 | 1.1 | 1.7 | 3.9 |
| Seven transmembrane MLO protein family (MLO6) | At1g61560 | 3.1 | 3.9 | 1.6 | 1.8 | 1.8 | 1.4 | 11.0 | 0.7 |
| Gly-rich protein | At3g04640 | 4.1 | 3.4 | 1.2 | 0.9 | 1.1 | 0.9 | 1.0 | 0.7 |
| Stress-related protein related | At1g67360 | 3.1 | 2.0 | 1.1 | 0.8 | 1.1 | 0.9 | 3.6 | 1.6 |
| Thaumatin family | At4g36010 | 2.3 | 4.5 | 1.6 | 1.6 | 1.2 | 1.8 | 14.1 | 3.9 |
| Cell wall modification | |||||||||
| BON1-associated protein 1 (BAP1) | At3g61190 | 3.3 | 2.5 | 1.4 | 1.8 | 0.8 | 0.9 | 1.8 | 0.8 |
| Cellulose synthase family (ATCSLE1) | At1g55850 | 1.6 | 3.1 | 1.0 | 1.7 | 0.8 | 1.8 | 1.1 | 1.1 |
| Glucosyltransferase related | At2g15480 | 4.4 | 6.7 | 0.9 | 1.2 | 1.1 | 1.7 | 7.2 | 4.9 |
| Glycosyltransferase family | At1g73880 | 0.9 | 3.6 | 0.9 | 1.8 | 0.8 | 1.3 | 0.9 | 1.0 |
| UDP-glycosyltransferase family | At1g07260 | 1.2 | 3.2 | 0.8 | 1.1 | 1.0 | 1.1 | 0.5 | 0.4 |
| Cinnamyl-alcohol dehydrogenase (CAD) family | At1g09500 | 1.5 | 7.2 | 0.6 | 1.3 | 0.5 | 1.3 | 0.5 | 1.8 |
| Xyloglucan endotransglycosylase (TCH4) | At5g57560 | 3.5 | 0.4 | 0.8 | 0.3 | 0.8 | 0.4 | 0.9 | 0.5 |
| Heat-shock response | |||||||||
| 17.6-kD heat-shock protein (AA 1-156) | At1g53540 | 6.3 | 13.5 | 1.5 | 1.5 | 1.3 | 1.4 | 20.6 | 32.3 |
| Class I heat-shock protein(HSP 17.4) | At3g46230 | 3.3 | 12.4 | 1.3 | 1.2 | 0.8 | 1.3 | 3.5 | 13.8 |
| Class II heat-shock protein | At5g12020 | 3.7 | 12.5 | 0.8 | 0.8 | 0.9 | 0.5 | 2.0 | 10.0 |
| Endomembrane-localized small heat-shock protein | At4g10250 | 5.9 | 5.4 | 1.8 | 1.6 | 1.1 | 1.2 | 1.0 | 4.9 |
| Heat-shock protein 17.6A (AT-HSP17.6A) | At5g12030 | 4.4 | 13.2 | 1.0 | 0.6 | 0.8 | 1.0 | 2.7 | 15.1 |
| Heat-shock protein family | At1g52560 | 8.7 | 28.1 | 1.4 | 0.7 | 0.9 | 1.3 | 1.6 | 18.2 |
| Heat-shock protein family | At5g37670 | 4.6 | 3.0 | 1.3 | 0.8 | 0.8 | 0.9 | 2.6 | 6.0 |
| Heat-shock protein family (HSP18.2) | At5g59720 | 2.4 | 4.7 | 1.3 | 1.8 | 1.1 | 0.9 | 1.7 | 12.1 |
| Heat-shock protein hsp70b | At1g16030 | 4.1 | 10.0 | 1.3 | 0.8 | 1.2 | 1.3 | 5.5 | 10.5 |
| Heat-shock protein hsp70t-2 | At2g32120 | 3.5 | 3.9 | 1.6 | 0.8 | 1.2 | 1.2 | 5.3 | 10.6 |
| Heat-shock protein, putative | At1g59860 | 5.4 | 4.8 | 1.4 | 0.9 | 1.3 | 1.3 | 20.2 | 8.8 |
| Heat-shock protein, putative | At2g20560 | 4.1 | 7.2 | 1.1 | 1.5 | 0.8 | 1.9 | 7.5 | 5.9 |
| Mitochondrion-localized small heat-shock protein | At4g25200 | 5.2 | 2.2 | 1.1 | 0.6 | 1.0 | 1.8 | 1.6 | 7.3 |
| Small heat-shock protein related | At2g19310 | 2.3 | 3.0 | 0.9 | 1.2 | 0.8 | 1.6 | 1.3 | 1.2 |
| Small heat-shock protein, chloroplast precursor (HSP21) | At4g27670 | 5.3 | 3.0 | 1.7 | 1.5 | 1.2 | 1.4 | 1.6 | 14.7 |
| Oxidative burst stress response | |||||||||
| Glutathione peroxidase, putative (AtGPX6) | At4g11600 | 1.5 | 3.2 | 0.8 | 1.1 | 1.0 | 1.4 | 3.0 | 4.5 |
| Glutathione S-conjugate ABC transporter (AtMRP1) | At1g30400 | 1.1 | 3.8 | 0.8 | 1.2 | 0.9 | 1.2 | 1.1 | 1.7 |
| Glutathione transferase, putative (GST21) | At2g29470 | 1.5 | 4.2 | 1.0 | 1.6 | 1.2 | 1.1 | 1.0 | 0.7 |
| Glutathione transferase, putative (GST6) | At2g47730 | 1.7 | 5.1 | 0.8 | 1.0 | 1.0 | 1.8 | 2.3 | 3.4 |
| Iron superoxide dismutase (FSD1) | At4g25100 | 3.1 | 2.5 | 1.0 | 0.9 | 0.9 | 1.0 | 1.0 | 0.6 |
| Group 4: Secondary Metabolism | |||||||||
| FAD-linked oxidoreductase family | At1g30700 | 1.6 | 7.9 | 0.4 | 0.6 | 0.3 | 0.3 | 4.0 | 3.7 |
| FAD-linked oxidoreductase family | At4g20860 | 3.7 | 6.6 | 1.1 | 1.4 | 1.1 | 1.1 | 6.0 | 2.3 |
| FAD-linked oxidoreductase family | At5g44360 | 2.5 | 4.5 | 1.1 | 1.4 | 1.0 | 0.7 | 1.0 | 1.1 |
| Cytochrome P450, putative (CYP72A15) | At3g14690 | 1.8 | 4.0 | 1.0 | 1.3 | 1.1 | 1.7 | 1.4 | 3.8 |
| Cytochrome P450, putative (CYP707A3) | At5g45340 | 3.2 | 0.3 | 0.5 | 0.3 | 1.0 | 0.9 | 0.5 | 0.2 |
| Group 5: Hormonal Response | |||||||||
| Auxin | |||||||||
| Auxin-induced protein family | At3g09870 | 4.5 | 0.7 | 1.0 | 0.8 | 1.1 | 0.9 | 0.6 | 0.4 |
| Auxin-induced protein family | At5g35735 | 4.1 | 3.4 | 1.0 | 1.0 | 0.9 | 1.0 | 6.0 | 1.8 |
| JA | |||||||||
| 12-Oxo-phytodienoate reductase (OPR2) | At1g76690 | 2.7 | 6.2 | 1.1 | 1.7 | 1.2 | 1.8 | 3.1 | 6.7 |
| Abscisic acid | |||||||||
| ABA-responsive protein related | At5g13200 | 2.8 | 3.2 | 1.6 | 1.1 | 1.6 | 1.3 | 8.6 | 4.1 |
| Group 6: Transporter | |||||||||
| ABC transporter family protein | At1g15520 | 1.7 | 18.7 | 0.9 | 1.0 | 0.9 | 1.1 | 3.0 | 16.1 |
| Ammonium transporter, putative (ATAMT1;2) | At1g64780 | 1.6 | 4.2 | 1.5 | 1.9 | 1.3 | 1.3 | 1.6 | 1.2 |
| High-affinity sulfate transporter related (SEL1) | At1g78000 | 0.7 | 10.1 | 0.9 | 0.9 | 1.2 | 1.1 | 0.4 | 1.2 |
| Mitochondrial carrier protein family | At2g22500 | 4.7 | 1.1 | 1.4 | 1.0 | 1.3 | 0.8 | 4.1 | 0.8 |
| Mitochondrial carrier protein family | At4g24570 | 3.9 | 0.4 | 0.7 | 0.3 | 0.5 | 0.3 | 1.1 | 0.4 |
| Nucleoporin 98-related protein | At1g59660 | 4.7 | 0.9 | 1.7 | 0.7 | 1.6 | 1.0 | 0.8 | 0.5 |
| Zinc transporter, putative (MTPa2) | At3g58810 | 1.2 | 3.6 | 0.8 | 1.4 | 1.0 | 1.2 | 2.3 | 2.7 |
| Others | |||||||||
| 60S ribosomal protein L10 (RPL10C) | At1g66580 | 1.2 | 3.8 | 1.0 | 1.3 | 0.9 | 1.6 | 3.5 | 10.2 |
| AAA-type ATPase family | At3g50930 | 6.3 | 1.2 | 1.1 | 0.8 | 1.7 | 1.1 | 1.3 | 0.7 |
| Carbonic anhydrase related | At2g28210 | 3.2 | 4.2 | 1.2 | 0.7 | 1.0 | 0.9 | 1.7 | 2.3 |
| DnaJ protein family | At3g08970 | 4.0 | 5.0 | 0.9 | 1.7 | 1.1 | 1.6 | 2.4 | 4.3 |
| Glycosyl hydrolase family 1 | At2g44460 | 0.9 | 6.1 | 1.3 | 1.7 | 0.9 | 1.3 | 1.3 | 1.6 |
| Glycosyl hydrolase family 1, β-glucosidase (DIN2) | At3g60140 | 1.2 | 3.1 | 1.5 | 1.3 | 1.0 | 1.3 | 0.2 | 0.3 |
| Heavy-metal-associated domain-containing protein | At5g52760 | 3.2 | 0.8 | 1.0 | 0.5 | 1.0 | 0.7 | 1.5 | 0.8 |
| Hydrolase, α/β fold family | At4g24160 | 4.2 | 4.1 | 1.2 | 1.3 | 1.1 | 1.8 | 6.1 | 3.2 |
| Lemir (miraculin) related | At1g17860 | 1.8 | 3.4 | 1.3 | 1.5 | 1.1 | 0.9 | 6.3 | 2.7 |
| Lys decarboxylase-related protein | At5g06300 | 1.3 | 5.3 | 0.8 | 1.7 | 0.8 | 1.1 | 1.0 | 1.4 |
| Nitrilase 4 (sp P46011) (NIT4) | At5g22300 | 1.2 | 3.9 | 1.1 | 1.7 | 1.0 | 1.9 | 1.2 | 1.8 |
| Phospholipid/glycerol acyltransferase family | At4g01950 | 3.2 | 0.7 | 0.7 | 0.7 | 0.6 | 0.5 | 1.9 | 0.6 |
| Pyridine nucleotide-disulfide oxidoreductase family | At3g44190 | 3.6 | 4.3 | 1.1 | 1.1 | 1.0 | 1.2 | 12.7 | 3.2 |
| Transferase family | At5g07870 | 7.0 | 4.7 | 1.7 | 1.6 | 1.1 | 1.5 | 2.0 | 1.8 |
| Pyridine nucleotide-disulphide oxidoreductase family | At5g22140 | 6.6 | 20.9 | 1.0 | 1.4 | 0.9 | 1.1 | 6.9 | 24.2 |
| Aldo/keto reductase family | At1g60730 | 1.1 | 4.6 | 0.9 | 1.4 | 0.9 | 1.8 | 1.8 | 4.1 |
| Aldo/keto reductase family | At1g60750 | 1.4 | 5.8 | 0.9 | 1.2 | 1.4 | 1.2 | 2.9 | 2.1 |
| Ubiquinol-cytochrome-c reductase-related protein | At5g25450 | 2.5 | 5.3 | 1.2 | 1.5 | 0.8 | 1.3 | 5.4 | 8.9 |
| Expressed and putative proteins are 49 | |||||||||