Article Figures & Data
Figures
- Fig. 1.
A representative scatter plot of the expression level of 8,200 genes, showing the reproducibility between GeneChip experiments. Total RNA was prepared from the control sample at the 0 time point, and labeled samples were independently synthesized and hybridized to the arrays. Note that a high correlation is observed, indicating the results are reproducible.
- Fig. 2.
Hierarchical cluster of the wounding-induced and -reduced genes using Spearman rank correlation, showing the early “signal gene clusters” and late “effector gene clusters.” Up-regulated gene clusters are indicated by red bars (signal gene clusters) or orange bars (effector gene clusters). Down-regulated gene clusters are indicated by the blue bar.
- Fig. 3.
A hypothetical model for early wound-responsive transcription factors to activate late responsive genes in wounding signal transduction pathways.
Tables
Gene Family Accession No. Fold1-a W0.51-b W6 Phosphatases MP2C-like protein phosphatase 2C CAB45796 37.16 Putative protein phosphatase 2C AAC31850 18.01 Protein phosphatase 2C-like protein CAA19874 6.15 Protein phosphatase 2C-like protein CAA16879 2.83 Protein phosphatase 2C BAA07287 2.18 Protein phosphatase 2C CAA05875 2.12 Receptor-like protein kinases (RLKs) Putative receptor protein kinase AAB80675 9.26 Similar to RLK AAB65477 8.15 Similar to RLK3 CAA18469 7.42 Similar to S-receptor kinase (BRLK) CAA20204 6.71 RLK3 CAA09731 5.61 Similar to RLK5 AAD40144 4.76 Similar to S-receptor kinase 8 precursor AAC18787 4.61 Putative protein kinase AAF07814 4.61 −2.07 Putative receptor protein kinase AAF07816 4.27 Similar to RLK3 CAB45516 4.27 Similar to wall-associated kinase 1 CAB41191 4.21 Protein kinase catalytic domain, AK2 CAA60510 3.58 Similar to RLK5 AAD32284 2.88 RLK CAA18465 2.41 Similar to S-receptor kinase (ARK1) AAC13905 2.26 Putative receptor-like protein kinase AAD28318 2.07 S-Like receptor protein kinase AAC13903 2.76 Similar to RLK AAC06160 −3.64 Putative RLK AAB82629 −2.05 Similar to ARK3 CAB44328 −2.24 Similar to CLV1 receptor kinase CAA16688 −2.44 Putative receptor protein kinase CAA19724 −5.25 Non-Receptor protein kinases Similar to NPK1 protein kinase AAC31848 8.23 Similar NAK protein kinase AAC95171 6.03 Ribosomal-protein S6 kinase (AtPK19) BAA07661 5.62 Protein kinase-like protein CAB44327 5.51 3.38 Protein kinase (APK2a) BAA24694 5.31 Protein kinase 6-like protein CAB51172 5.21 Putative protein kinase AAF26067 3.31 Similar to Pti1 kinase AAC34243 3.09 Similar to APK1 protein kinase CAA20030 3.05 Similar to protein kinase NAK AAB97121 3.02 Similar to CBL-interacting protein kinase AAC16938 2.59 3.81 Calcium-dependent protein kinase 1 AAF27092 2.05 Hypothetical Ser-Thr protein kinase AAD25942 2.03 Similar to CTR1, MAP3K family AAD30219 4.64 Similar to EDR1, MAP3K family CAA19821 4.37 Putative protein kinase AAC09037 −2.71 Casein kinase I (CKI2) CAA55397 −2.94 AK23, protein kinase catalytic domain CAA60531 −2.08 Putative protein kinase CAB10237 −2.33 Contain protein kinase catalytic domain AAD26873 −3.35 Calcium-binding proteins Similar to CCD-1 CAA19722 22.18 Calmodulin (CAM)-related protein (TCH2) AAB82713 7.52 Putative calmodulin like, MSS3 AAB64310 4.71 Calmoudulin-like protein, CALL_ARATH AAC78532 4.15 Calmodulin-like protein CAB42906 3.01 4.31 Putative calcium-binding protein (RD20) AAB80656 3.36 Putative calmodulin (CAM9) CAB41312 −2.38 GTP-binding proteins Extra-large G-protein like CAB36716 3.66 Similar to GTP-binding protein CAB38902 3.55 Similar to GTP exchanger factor AAB61488 3.47 SGP1 monomeric G-protein CAB54517 3.18 GTP-binding protein Rab7 AAC25512 −2.77 Phosphatidylinositol (PI) signaling molecules PI 5-phosphatase like AAD10829 2.95 Inositol trisphosphate 5-phosphatase CAB59428 2.68 Similar to PI 5-phosphatase AAD46036 13.42 PI synthase (PIS1) AAF16562 −2.02 AP2/EREB-type transcription factors Putative EREBP protein AAC31840 53.77 DREB1B/CBF1 BAA33435 38.89 EREBP homolog CAB36718 26.11 Similar to AtERF-4 AAF16756 20.61 AtERF-5 BAA32422 6.42 AtERF-4 AAF34830 6.05 EREBP-4 like protein CAB10530 5.77 AtERF-1 BAA32418 5.71 Similar to TINY isolog AAC25505 4.78 RAV2 BAA34251 3.74 −2.31 CRT/DRE binding factor 2 (CBF2) AAD15976 2.14 AP2 domain containing protein RAP2.6 AAC36019 105.25 AP2 domain transcription factor AAD20907 14.33 AP2 domain containing protein RAP2.9 AAC49775 3.61 AP2 domain containing protein RAP2.4 AAC49770 2.81 AP2 domain transcription factor AAD20668 −2.18 AP2 domain containing protein RAP2.7 AAD21489 −2.74 Putative AP2 domain protein CAA23041 −2.85 Putative AP2 transcription factor AAD32841 −3.11 WRKY-type transcription factors AtWRKY40 AAF14671 25.52 AtWRKY33 AAC67339 15.12 AtWRKY53 CAA23047 13.24 AtWRKY22 AAB61016 4.18 AtWRKY11 CAB45914 3.01 AtWRKY15 AAB87100 2.81 AtWRKY60 AAD23013 2.63 MYB-type transcription factors AtMYB15 CAA74603 17.88 AtMYB51 CAB09206 8.42 AtMYB77/AtMYBR2 CAA74604 7.91 AtMYB96 AAD53106 4.18 2.52 AtMYB73 CAB16756 3.36 −3.01 AtMYB44/AtMYBR1 CAB09200 2.48 AtMYB20 AAC83591 −2.01 −2.42 AtMYB28 CAB09183 −2.14 AtMYBL2 CAA92280 −2.68 AtMYB106 AAF26160 −3.32 AtMYB16 CAB09174 −3.62 AtMYB3 AAC83581 −4.14 AtMYB4 AAC83582 −5.67 Zinc finger-type transcription factors Zinc finger protein (AtRZAT7) CAA67234 52.01 Putative C2H2-type zinc finger protein AAC98070 18.91 Putative CCCH-type zinc finger protein AAF18728 15.96 −2.33 C2H2 zinc finger protein (AtZat12) CAA67232 11.64 2.17 Putative Cys-3-His zinc finger protein AAD25930 11.17 −2.71 Salt-tolerance STZ/ZAT10 protein AAF24959 10.21 RING zinc finger protein (ATL2) AAC77829 7.08 Similar to salt tolerance STZ/ZAT10 AAB80922 7.65 2.72 RING-H2 finger protein (RHA3b) AAC68674 4.46 22.21 Putative zinc finger protein (PMZ) AAD37511 4.05 3.31 Similar to zinc-binding protein (PWA33) AAC24052 3.75 3.18 Similar to GATA transcription factor 3 CAB41103 3.01 RING-H2 zinc finger protein (ATL6) AAD33584 2.92 Putative DOF zinc finger protein AAD21486 2.17 Putative CCCH-type zinc finger protein AAC62135 −2.04 RING zinc finger protein (RMA1) AAD11593 −2.26 Putative CCCH-type zinc finger protein AAC42256 −2.32 C2H2-type zinc finger protein (ZFP8) AAA87304 −3.22 Other-type transcription factors Putative bHLH transcription factor AAAC63587 10.69 Similar to bHLH transcription factor AAD22130 2.14 Similar to bHLH factor GBOF-1 CAB16839 −2.03 −2.55 Heat shock transcription factor 4 AAC31756 6.67 4.58 Heat shock transcription factor 21 AAC31792 5.68 Homeodomain zipper protein (AtHB-7) AAC69925 2.89 Homeodomain zipper protein (AtHB-12) AAC39462 2.28 Homeodomain zipper protein (AtHB-16) AAD46064 −2.33 Putative Function Accession No. Fold2-a W0.52-b W6 Pathogenesis-related genes Similar to NDR1/HIN1-like protein 3 AAC77866 18.02 Similar to Hs1pro-1 AAB95285 12.08 Similar to regulatory protein NPR1 CAA19683 5.07 Similar to Mlo proteins AD25552 4.51 Putative lectin like protein AAC27148 3.88 Non-race-specific disease resistance protein (NDR1) AAB95208 3.71 Similar to Avr9/Cf-9 rapidly elicited protein 137 AAD25764 3.69 Resistance protein RPP5-like CAA16929 2.47 Disease resistance protein RPP1-WsC AAC72979 2.13 Similar to Mlo proteins AAC28997 14.03 Similar to disease resistance protein Cf-2.2 AAC12833 4.88 Putative disease resistance protein AAD26901 4.44 AIG1, disease resistance protein AAC49282 3.66 Disease resistance RPP5 like protein CAB10461 −3.77 Putative β-1,3-glucanase AAD15611 3.61 β-1,3-glucanase-like protein CAA16806 2.12 Putative β-1,3-glucanase CAA18827 −2.61 Putative endochitinase AAB64044 16.35 Class IV chitinase CAA74930 8.42 Putative endochitinase AAB64049 2.79 Similar to class I chitinases AAC72865 2.26 Putative antifungal protein, AFP3_ARATH AAC31244 −2.78 −2.15 Thaumatin-like protein, PR-5 AAF21072 −2.08 Putative protease inhibitor AAC79626 4.59 Putative trypsin inhibitor AAB64325 4.13 Oxidative burst Peroxidase ATP24a CAA72484 15.41 Peroxidase ATP15a CAA67551 5.25 11.75 Respiratory burst oxidase protein D AAC39479 4.81 Putative l-ascorbate oxidase CAA18769 2.71 CTF2B, similar to monooxygenase 2 AAD09952 2.51 GA 2-oxidase CAB41008 2.07 2.31 Similar to glutathioneS-transferase AAD32888 5.91 Putative glutathione S-transferase AAC95194 5.45 Peroxidase ATP2a CAA66863 3.46 Putativep-hydroxyphenylpyruvate dioxygenase AAF24813 3.33 Putative glutathioneS-transferase AAC95192 3.28 Similar to aldehyde reductase AAC62136 3.22 GlutathioneS-transferase CAA74639 2.72 Putative amine oxidase AAD22129 2.67 Putative copper amine oxidase AAD23730 2.23 Putative ferredoxin AAD15602 2.21 Putative glutathioneS-transferase AC95196 2.11 Glutathione reductase AAB67841 2.07 Catalase 3 AAC49807 −3.27 Cytochrome P450 Putative cytochrome P450 AAC02748 6.31 Putative cytochrome P450 AAB87109 6.25 Putative cytochrome P450 AAC06158 4.22 Cytochrome P450 monooxygenase BAA28534 −2.21 Phenylpropanoid biosynthesis Putative leucoanthocyanidin dioxygenase AAC27173 13.66 Cinnamyl-alcohol dehydrogenase ELI3-2 CAB37539 11.75 Similar to cinnamyl alcohol dehydrogenase AAC33210 8.89 Cinnamyl alcohol dehydrogenase-like protein CAA17549 8.31 Putative cinnamoyl-CoA reductase AAB80681 2.49 Putative chorismate mutase/prephenate dehydratase AAC73018 −2.13 Flavonoid 3′,5′-hydroxylase-like protein CAB45977 −6.83 TRP pathway Phosphoribosylanthranilate isomerase AAD38141 2.72 Strictosidine synthase AAB40594 2.67 TRP synthase α-chain AAC49117 2.11 Anthranilate synthase, α-subunit AAC35228 2.05 AnthranilateN-benzoyltransferase-like protein AAB95283 −2.14 2.01 Putative chorismate mutase/prephenate dehydratase AAC73018 −2.13 Berberine biosynthesis Putative berberine bridge enzyme AAD25759 6.51 9.25 Berberine bridge enzyme-like protein CAB42588 2.61 6.14 Berberine bridge enzyme-like protein CAB45881 2.32 3.27 Tyr transaminase-like protein CAA23026 2.55 Putative berberine bridge enzyme AAC12821 2.54 Putative Tyr transaminase AAD23027 2.08 Cell wall modification Xyloglucan endotransglycosylase-related protein AAB18367 10.50 Xyloglucan transglycosylase-related protein (TCH4) AAC05572 4.08 2.18 Similar to TCH4 gene AAC27142 4.06 Similar to xyloglucan fucosyltransferase FT1 AAD22285 3.91 Glycosyltransferase-like protein CAB62445 2.46 Putative glucosyltransferase AAC16958 3.13 Putative glucosyltransferase AAB64024 2.96 Putative xyloglucan endotransglycosylase AAD31572 2.19 Similar to pectinesterase AAC19280 3.37 3.41 Putative pectin methylesterase AAC02974 3.11 4.01 Pectinesterase 1 AAF02857 2.39 Similar to pectinesterase CAB51210 16.91 Putative pectinesterase AAB82640 3.35 Putative pectin methylesterase AAC02973 2.26 Putative pectate lyase CAA22985 −2.28 Cellulose synthase isolog AAB63623 4.88 Cellulose synthase like protein CAB10434 −2.01 2.23 UDP-Glc 4-epimerase-like protein CAB45812 11.61 Putative UDP-galactose-4-epimerase AAD25749 2.18 2.15 Extensin-like protein CAA22152 13.41 Extensin like protein, pEARLI 1 CAB41718 −2.03 4.74 pEARLI 1-like protein CAB41717 6.11 Expansin At-EXP1 AAB38070 −2.16 Putative expansin AAB87577 −3.29 Gly-rich protein AAA32722 12.70 Putative Pro-rich protein AAD29802 2.62 Gly-rich RNA-binding protein AtGRP2 like CAB36849 −2.44 Gly-rich protein, atGRP-2 AAB24074 −3.26 Putative Function Accession No. Fold3-a W0.53-b W6 Cold/drought responsive DREB1B/CBF1 BAA33435 38.89 CRT/DRE binding factor 2 (CBF2) AAD15976 2.14 LEA D113 homolog type 1 CAA63008 36.76 LEA76 homolog type 1 CAA63012 36.45 Dehydrin AAB00374 15.36 Cor78/Rd29A AAA32775 12.01 Cor15b precursor AAD23000 6.63 Cor47/Rd17 BAA23547 5.54 Lti29 CAA62448 4.88 Similar to LEA14 AAC62908 4.87 Rd20 AAB80656 3.36 Homeodomain transcription factor (AtHB-7) AAC69925 2.89 Putative dessication-related protein LEA14 CAA71174 2.72 Rd22 BAA01546 2.44 Homeodomain transcription factor (AtHB-12) AAC39462 2.28 Kin1 CAA35838 2.23 Cold-regulated cor6.6/kin2 CAA38894 2.05 Salt/abscisic acid responsive Similar to protein phosphatase MP2C CAB45796 37.17 Salt tolerance zinc finger protein (STZ/ZAT10) AAF24959 10.21 Similar to salt tolerance factor STZ/ZAT10 AAB80922 7.65 2.72 Ribosomal protein S6 kinase homolog (AtPK19) BAA07661 5.63 Putative Suc-proton symporter (AtSUC3) AAC32907 2.42 Trehalose-6-phosphate phosphatase-like CAA22164 2.11 Calcium-dependent protein kinase 1 (CDPK1) AAF27092 2.05 Aquaporin/MIP-like protein CAB41102 4.92 Putative Pro transporter AAD24641 3.13 Pro transporter (AAP4) CAA54631 2.85 Suc transport protein (SUC1) AAF34305 2.56 Aquaporin (PIP2a) AAD18142 2.51 Aquaporin (PIP1a) CAA53475 2.39 Δ1-Pyrroline-5-carboxylate synthetase (ATP5CS) BAA06864 2.29 Similar to trehalose-6-phosphate synthase AAC24048 2.28 Suc synthase CAA50317 2.24 Putative ABI1 and ABI2 homolog CAA05875 2.12 Heat shock responsive HSF-like protein CAA16745 7.25 HSF 4 AAC31756 6.67 4.58 HSF 21 AAC31792 5.68 Heat shock protein (HSP) 17.6-II CAA45039 11.01 HSP 70 CAA05547 4.51 HSP 17.6A CAA74399 3.72 Hsc70-G8 protein CAA70105 2.81 DnaJ-like protein CAA18498 2.45 Hsc70-G7 protein CAA70111 2.18 HSP 83 AAA32822 2.15 Response Putative Function Classification Treatment Response Early (30 min) Heat shock transcription factor-like protein (HSF21: CAA16745) 1 = Stress Wounding 1 h after treatment 2 = Pathogen Pseudomonas syringae 3 h after treatment 3 = Virus Tobacco rattle virus ? 4 = Others Senescent ? Constitutive (30 min and 6 h) Heat shock transcription factor 4 (HSF4: AAC31756) 1 = Stress Wounding 0.5 and 1 h after treatment Detachment 12 h after treatment Osmotic stress 3 and 27 h after treatment Electroporation shock 17 h after treatment 2 = Pathogen P. syringae 3, 6, 9, 12, 27, 30, and 48 h after treatment Peronospora parasitica 12 and 48 h after treatment 3 = Virus Turnip mosaic virus 28 and 92 h after treatment Tobacco rattle virus 92 h after treatment Cucumber mosaic virus 92 h after treatment 4 = Chemical Benzothiadiazole (BTH) 48 and 72 h after treatment Jasmonic acid 40 h after treatment β-Aminobutyric acid (BABA) 72 h after treatment 5 = Others Light 4, 8, 12, 16, 20, 24, and 40 h after treatment Cold 3 and 27 h after treatment Late (6 h) Heat shock protein 70 and 17.6A (HSP70 and 17.6A CAA05547 and CAA74399) 1 = Stress Osmotic 3 and 27 h after treatment Electroporation shock ? 2 = Pathogen P. parasitica 48 h after treatment 3 to 48 h after treatment 3 = Virus Oil seed virus 28 h after treatment Tobacco rattle virus 52 h after treatment Turnip vein clearing virus 52 h after treatment Turnip mosaic virus 92 h after treatment 4 = Chemical γ-Aminobutyric acid (GABA) 24 h after treatment Jasmonic acid 40 h after treatment Salicylic acid 2 h after treatment BTH 48 and 72 h after treatment 5 = Others Light 24 h after treatment Cold 3 and 27 h after treatment Putative Function Accession No. Fold5-a W0.55-b W6 Jasmonic acid pathway Putative allene oxide synthase AAD03574 2.72 3.94 Phospholipase like protein AAC37472 2.45 Putative phospholipase AAC27833 2.06 Putative GDSL motif lipase/hydrolase AAD25823 3.98 Lipoxygenase CAB56692 3.68 12-Oxophytodienoate reductase (OPR1) AAC78440 2.16 Ethylene pathway Putative EREBP protein AAC31840 53.77 EREBP homolog CAB36718 26.11 ACC synthase (AtACS-6) CAB51412 23.66 ACC synthase AAC63850 21.26 Similar to AtERF-4 AAF16756 20.61 AtERF-5 BAA32422 6.42 AtERF-4 AAF34830 6.05 EREBP-4 like protein CAB10530 5.77 AtERF-1 BAA32418 5.71 Similar to senescense-associated protein AAF18611 4.31 Senescense-associated protein AAD20613 8.72 Auxin pathway Putative auxin-regulated protein AAB82641 6.25 Auxin-responsive GH3-like protein AAD23040 2.42 Putative auxin-regulated protein AAC69926 −2.55 Putative GH3-like protein AAD14468 −3.29 Auxin-induced protein-like CAB38618 −3.83 −2.29 SAUR-AC1= small auxin up RNA AAB30527 −4.15 −2.31 Putative auxin-induced protein CAB38620 −7.13 −3.86 Auxin-responsive protein IAA2 AAB97164 −2.12 Match to Arabidopsis IAA3 AAB70452 −2.12 Auxin-induced protein (IAA20) AAC34236 −2.16 Similar to auxin-induced protein AAB62852 −2.18 Putative auxin-regulated protein AAD29795 −2.54
Data Supplement for PLANT PHYSIOLOGY: Volume 129, Issue 2 -- Page 661
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Transcriptional Profiling Reveals Novel Interactions between Wounding, Pathogen, Abiotic Stress, and Hormonal Responses in Arabidopsis
