Table 4.
Transcripts associated with auxin-responsive metabolic processes.
| ID | Gene Number | ProbeSet No. | Average SLR change after transfer to hormone-containing medium | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 0 h | 0.5 h | 1 h | 2 h | 4 h | 8 h | 12 h | 24 h | |||
| IAA metabolism, transport, signaling | ||||||||||
| DAO1* | AT1G14130 | 262653_at | −0.27 | 0.23 | −0.15 | 0.32 | 0.03 | −0.72 | −0.47 | 0.08 |
| DAO2* | AT1G14120 | 262608_at | 0.02 | −0.26 | −1.00 | −0.54 | −1.27 | −1.57 | −1.28 | −0.55 |
| GH3.1 | AT2G14960 | 266611_at | −0.02 | 2.09 | 2.05 | 3.56 | 3.95 | 4.12 | 3.41 | 2.60 |
| GH3.3* | AT2G23170 | 245076_at | −0.56 | 4.94 | 4.49 | 5.58 | 6.10 | 6.08 | 4.67 | 3.94 |
| GH3.5 | AT4G27260 | 253908_at | −0.10 | 2.97 | 3.13 | 3.89 | 4.00 | 4.49 | 4.12 | 4.01 |
| GH3.6* | AT5G54510 | 248163_at | 0.00 | 2.00 | 1.98 | 2.51 | 2.41 | 2.84 | 2.52 | 2.01 |
| CYP79B2† | AT4G39950 | 252827_at | −0.23 | 0.24 | −0.56 | −1.61 | −0.54 | −0.15 | −0.15 | 0.04 |
| CYP79B3† | AT2G22330 | 264052_at | −0.08 | −0.17 | −0.25 | −1.30 | −1.09 | −0.49 | −0.24 | −0.37 |
| NIT1, NIT2 | AT3G44310 AT3G44300 | 252678_s_at | −0.05 | −0.24 | −0.22 | 0.29 | −0.16 | −0.73 | −1.08 | −0.53 |
| UGT74E2* | AT1G05680 | 263231_at | 0.06 | −0.20 | −1.22 | −0.57 | −1.16 | −2.34 | −2.54 | −1.68 |
| PIN1 | AT1G73590 | 259845_at | −0.02 | 1.04 | 1.32 | 1.53 | 1.17 | 0.48 | 0.17 | 0.34 |
| PIN3 | AT1G70940 | 262263_at | −0.14 | 1.33 | 1.20 | 1.27 | 1.53 | 1.31 | 1.17 | 0.57 |
| PIN7 | AT1G23080 | 264900_at | 0.00 | 0.89 | 1.40 | 1.76 | 1.67 | 1.29 | 1.34 | 0.83 |
| ASP4 | AT1G62800 | 262646_at | −0.17 | −0.10 | −0.06 | −0.56 | −0.82 | −0.57 | −0.31 | −0.02 |
| Ethylene metabolism | ||||||||||
| ACO1* | AT2G19590 | 265948_at | 0.03 | −0.20 | 0.33 | 1.00 | 1.14 | 0.93 | 0.84 | 0.68 |
| ACO3* | AT1G12010 | 264346_at | −0.02 | −0.08 | 0.04 | 0.47 | 0.74 | 1.30 | 0.94 | 0.90 |
| ACO4 | AT1G05010 | 265194_at | −0.08 | 0.14 | 0.00 | −0.23 | −0.78 | −0.52 | −0.38 | 0.47 |
| ACS5 | AT5G65800 | 247159_at | 0.09 | −0.22 | −0.20 | −0.58 | −0.53 | −0.59 | −0.62 | −0.40 |
| ACS6 | AT4G11280 | 254926_at | −0.05 | 1.36 | 0.61 | 0.97 | 0.38 | 0.00 | −0.99 | 0.45 |
| ACS7 | AT4G26200 | 253999_at | −0.17 | 0.51 | −0.33 | −0.41 | −0.26 | −0.74 | −0.88 | −0.34 |
| ACS8 | AT4G37770 | 253066_at | 0.07 | 0.91 | 0.61 | 1.14 | 1.03 | 0.65 | 0.20 | 0.27 |
| ACS9 | AT3G49700 | 252279_at | 0.12 | 1.05 | 1.38 | 2.08 | 2.27 | 2.00 | 2.15 | 1.31 |
| ACS11* | AT4G08040 | 255177_at | 0.05 | 1.83 | 1.33 | 1.52 | 1.77 | 0.96 | 0.07 | 0.26 |
| Glucosinolate metabolism, including indole glucosinolate biosynthesis | ||||||||||
| BCAT4* | AT3G19710 | 257021_at | −0.32 | 0.09 | −0.35 | 0.34 | 0.24 | 0.21 | 1.19 | 0.75 |
| CYP79F1, CYP79F2 | AT1G16410 AT1G16400 | 262717_s_at | −0.20 | 0.39 | −0.12 | 0.12 | 0.19 | −0.03 | 0.62 | 0.39 |
| CYP79B2† | AT4G39950 | 252827_at | −0.23 | 0.24 | −0.56 | −1.61 | −0.54 | −0.15 | −0.15 | 0.04 |
| CYP79B3† | AT2G22330 | 264052_at | −0.08 | −0.17 | −0.25 | −1.30 | −1.09 | −0.49 | −0.24 | −0.37 |
| CYP81F2* | AT5G57220 | 247949_at | −0.48 | −0.26 | −0.64 | −0.81 | 0.45 | −0.40 | −0.66 | −1.88 |
| CYP83A1* | AT4G13770 | 254687_at | −0.15 | 0.01 | −0.02 | 0.31 | 0.34 | 0.03 | 0.96 | 0.54 |
| UGT74B1 | AT1G24100 | 264873_at | −0.27 | 0.29 | −0.36 | −0.73 | −0.85 | −0.50 | −0.19 | 0.23 |
| Phenylpropanoid Metabolism | ||||||||||
| General | ||||||||||
| PAL1 | AT2G37040 | 263845_at | 0.01 | −0.19 | −0.45 | −0.59 | −0.63 | −0.70 | −0.57 | −0.21 |
| PAL2 | AT3G53260 | 251984_at | 0.01 | −0.12 | −0.36 | −0.24 | −0.33 | −0.80 | −0.63 | −0.47 |
| PAL4* | AT3G10340 | 259149_at | 0.06 | −0.17 | −0.39 | −0.84 | −1.05 | 0.30 | 0.02 | −0.14 |
| 4CL1 | AT1G51680 | 256186_at | 0.13 | −0.05 | −0.43 | −0.55 | −0.73 | −0.35 | −0.40 | −0.04 |
| 4CL3* | AT1G65060 | 261907_at | 0.18 | −0.34 | −0.27 | −0.46 | −0.61 | −0.79 | −0.30 | −0.58 |
| Hydroxycinnamate/lignin metabolism | ||||||||||
| CCR2 | AT1G80820 | 261899_at | 0.01 | −0.22 | −0.95 | −0.38 | −0.17 | −0.33 | 0.09 | −0.21 |
| F5H/ CYP84A1* | AT4G36220 | 261899_at | −0.17 | 0.23 | 0.66 | −0.23 | −0.39 | −0.10 | 0.45 | 0.76 |
| CYP84A4 (F5H activity) | AT5G04330 | 245710_at | −0.07 | −0.25 | −0.15 | −0.64 | −0.70 | −0.62 | −0.59 | −0.35 |
| CCOAMT* | AT1G67980 | 260015_at | −0.50 | 0.17 | −0.98 | −0.10 | 0.65 | 0.54 | 0.54 | −0.97 |
| CCOAOMT7* | AT4G26220 | 253985_at | 0.27 | −0.29 | −0.07 | 0.13 | −0.17 | −1.11 | −0.97 | −1.07 |
| ALDH2C4* | AT3G24503 | 258140_at | −0.15 | 0.07 | 0.12 | 0.72 | 0.88 | 0.33 | 0.30 | −0.29 |
| CAD-like | AT1G30760 | 264527_at | 0.00 | 0.00 | 0.31 | 1.58 | 2.52 | 4.32 | 4.52 | 3.50 |
| CAD6 | AT4G37970 | 253017_at | 0.19 | −0.46 | −0.89 | −0.18 | 0.77 | 0.84 | 0.79 | 0.88 |
| CAD8 | AT4G39330 | 252943_at | 0.03 | 0.12 | −0.31 | 0.20 | 0.15 | 0.33 | 0.66 | 1.50 |
| Flavonoid | ||||||||||
| CHS | AT5G13930 | 250207_at | 0.34 | −0.53 | −0.36 | −0.33 | −0.45 | −0.72 | 0.51 | −0.76 |
| CHI* | AT2G43570 | 260568_at | −0.32 | 0.26 | −0.94 | 0.38 | 0.53 | −0.05 | 0.15 | −0.03 |
| F3H* | AT3G51240 | 252123_at | 0.31 | −0.53 | −0.55 | −0.82 | −1.04 | −1.03 | −0.02 | −0.60 |
| F3’H* | AT5G07990 | 250558_at | 0.31 | −0.54 | −0.50 | −0.58 | −0.34 | −0.55 | −0.07 | −0.54 |
| UGT71C3* | AT1G07260 | 256053_at | −0.01 | −0.36 | −0.43 | −0.30 | 0.11 | 0.43 | 0.64 | 0.65 |
| Lipid Metabolism | ||||||||||
| Fatty acid metabolism | ||||||||||
| FAH1 | AT2G34770 | 267318_at | 0.23 | −0.16 | −0.55 | −0.92 | −0.88 | −0.56 | −0.37 | −0.48 |
| ACC2* | AT1G36180 | 256459_at | 0.13 | −0.29 | −0.24 | 0.04 | −0.29 | −0.61 | −0.72 | −0.17 |
| BCCP2 | AT5G15530 | 246565_at | 0.15 | −0.17 | 0.08 | −0.28 | −0.45 | −0.42 | −0.57 | −0.61 |
| NBRFSP | AT4G13180 | 254759_at | −0.07 | 0.83 | 0.53 | 1.11 | 0.63 | −0.26 | −0.56 | −0.05 |
| Phosphatidylcholine metabolism | ||||||||||
| PLDALPHA1 | AT3G15730 | 258226_at | 0.03 | −0.01 | 0.24 | 0.13 | 0.26 | 0.27 | 0.59 | 0.32 |
| PLDGAMMA1* | AT4G11850 | 254847_at | −0.12 | 0.09 | 0.10 | 0.18 | 0.70 | 0.39 | 0.33 | 0.35 |
| PLDDELTA | AT4G35790 | 253120_at | 0.06 | −0.15 | −0.16 | −0.60 | −1.06 | −0.59 | −0.44 | −0.06 |
| NPC3 | AT3G03520 | 259169_at | −0.11 | 0.04 | −0.31 | −1.20 | −0.88 | −0.08 | −0.03 | 0.15 |
| NPC4, NPC5* | AT3G03540 AT3G03530 | 259221_s_at | 0.27 | −0.13 | −0.28 | −0.16 | 0.07 | 0.25 | 0.83 | −0.10 |
| LCAT4 | AT4G19860 | 254547_at | 0.04 | −0.30 | −0.11 | −0.28 | −0.69 | −0.17 | −0.12 | 0.10 |
| PLA2-ALPHA | AT2G06925 | 266500_at | 0.12 | 0.16 | 0.00 | −0.15 | 0.15 | 0.63 | 1.02 | 0.66 |
| PLA-IBETA2 | AT4G16820 | 245447_at | −0.03 | 0.64 | 0.06 | 0.43 | 1.01 | 0.88 | 0.59 | 0.34 |
| PLP1, PLAIVA* | AT4G37070 | 246252_s_at | −0.04 | −0.37 | −0.36 | −1.28 | −1.20 | −0.69 | −0.71 | −0.68 |
Shown are genes having average log two-fold values relative to time-matched controls of ≥ 0.5 or ≤ −0.5 (~1.4 or −1.4-fold differences) in all three biological replicates at one or more sampling times (data from 11,12), with values meeting these criteria shown in bold and are underlined. Positive numbers indicate elevated levels and negative numbers indicate reduced levels relative to the untreated controls. The full list of genes examined for each class with values for each biological replicate are provided in Datafile S5. † denotes genes that participate in indole glucosinolate biosynthesis and thus are listed under two categories. Asterisks identify genes that meet the criteria for change in response to both auxin and ethylene. Enzyme abbreviations are as follows: 4CL (4-coumaroyl coenzyme A ligase), ACC (acetyl-CoA carboxylase), ACO (ACC oxidase), ACS (ACC synthase), ALDH (aldehyde dehydrogenase), ASP (aspartate aminotransferase), BCAT (branched-chain-amino-acid aminotransferase), CAD (cinnamyl-alcohol dehydrogenase), CAT (lecithin-cholesterol acyltransferase-like), CCOAMT (caffeoyl-CoA O-methyltransferase), CCoAOMT7 (caffeoyl-coenzyme A O-methyltransferase), CHI (chalcone isomerase), CHS (chalcone synthase), DAO (DIOXYGENASE FOR AUXIN OXIDATION), F3H (flavanone 3-hydroxylase), F3’H (flavonoid 3’-hydroxylase), FLS (flavonol synthase), GH (GRETCHEN HAGEN), NIT (nitrilase), NPC (non-specific phospholipase C), PAL (phenylalanine ammonia-lyase), PLA (phospholipase A), PLD (phospholipase D), PLP (patatin-like protein), UGT (uridine diphosphate-glycosyltransferase).