Table II. Genes comprising RM1.
Boldface values indicate genes with the strongest repression upon Pi deficiency. Fold changes are based on the differences in expression level between Pi-deficient and Pi-sufficient plants. Dashes indicate not differentially expressed at this time point. Data represent means from three biological replicates. The numbers in parentheses are P values adjusted for multiple testing by the method of Benjamini and Hochberg (1995).
| Locus | Annotation | Molecular Function | Fold (Log2) |
||
| 1 h | 6 h | 24 h | |||
| At1g01720 | ANAC002 (ATAF1) | Sequence-specific DNA-binding transcription factor activity, transcription activator activity | 1.36 (0.34) | 1.33 (0.13) | 1.43 (0.37) |
| At5g63790 | ANAC102 | Sequence-specific DNA-binding transcription factor activity | 1.81 (0.07) | 1.47 (0.05) | 1.06 (0.50) |
| At3g49530 | ANAC062 | Sequence-specific DNA-binding transcription factor activity | 1.23 (0.0007) | 1.16 (0.0005) | – |
| At1g77450 | ANAC032 | Sequence-specific DNA-binding transcription factor activity | 1.14 (0.58) | 1.81 (0.08) | 1.25 (0.59) |
| At1g62300 | WRKY6 | Sequence-specific DNA-binding transcription factor activity | – | 1.63 (0.12) | – |
| At4g31800 | WRKY18 | Sequence-specific DNA-binding transcription factor activity | 2.51 (1.74E-05) | 1.03 (0.01) | – |
| At4g18170 | WRKY28 | Sequence-specific DNA-binding transcription factor activity | – | 1.51 (0.09) | 1.72 (0.25) |
| At1g80840 | WRKY40 | Sequence-specific DNA-binding transcription factor activity | 1.97 (0.001) | 2.16 (0.0003) | – |
| At2g46400 | WRKY46 | Sequence-specific DNA-binding transcription factor activity | 1.35 (0.19) | 2.41 (0.002) | – |
| At5g49520 | WRYY48 | Sequence-specific DNA-binding transcription factor activity | – | 1.50 (0.007) | 1.01 (0.26) |
| At4g17500 | ATERF-1 | Sequence-specific DNA-binding transcription factor activity | 1.10 (0.11) | 1.54 (0.005) | – |
| At5g47220 | ERF2 | DNA binding | 1.52 (0.16) | 2.02 (0.01) | – |
| At3g06490 | MYB108 | Sequence-specific DNA-binding transcription factor activity | – | 1.84 (1.79E-05) | 1.38 (0.001) |
| At3g50260 | CEJ1 | Sequence-specific DNA-binding transcription factor activity | – | 1.31 (0.10) | 1.26 (0.40) |
| At1g19180 | JAZ1, TIFY10A | Protein binding | – | 1.29 (0.01) | – |
| At1g22810 | ERF/AP2 transcription factor family | DNA binding | 1.44 (0.004) | – | – |
| At2g44840 | ERF13 | Sequence-specific DNA-binding transcription factor activity | 1.72 (0.01) | 1.66 (0.005) | – |
| At3g53600 | Zinc finger (C2H2 type) family protein | Nucleic acid binding, zinc ion binding | – | 1.44 (0.01) | – |
| At1g76680/At1g76690 | OPR1/OPR2 | 12-Oxophytodienoate reductase activity | 1.67 (0.19) | 1.14 (0.22) | – |
| At5g54490 | PBP1 | Calcium ion binding, protein binding | 2.25 (0.18) | 1.93 (0.10) | – |
| At5g42380 | CML39 | Calcium ion binding | 2.42 (0.05) | 1.80 (0.06) | – |
| At2g41640 | Transferase | Transferase activity | 2.54 (0.0002) | 1.16 (0.03) | – |
| At3g22910 | ATPase E1-E2 type family protein | Calmodulin binding | – | 3.29 (5.61E-06) | – |
| At3g61190 | BAP1 | Phospholipid binding, protein binding | 1.46 (0.12) | 1.44 (0.04) | – |
| At3g01830 | Calcium-binding EF-hand family protein | Calcium ion binding | -- | 1.65 (0.0004) | – |
| At5g59820 | ZAT12 | Nucleic acid binding, zinc ion binding | 1.30 (0.25) | 2.25 (0.005) | 1.18 (0.41) |
| At3g55980 | SZF1 | Sequence-specific DNA-binding transcription factor activity | 1.11 (0.06) | – | – |
| At5g64250 | Aldolase-type TIM barrel family protein | Nitronate monooxygenase activity | – | 1.50 (0.0006) | – |
| At1g17180 | ATGSTU25 | Glutathione transferase activity | – | 3.34 (0.001) | – |
| At4g01870 | TolB protein related | Not assigned | – | 2.80 (0.003) | – |
| At3g28340 | GATL10 | Polygalacturonate 4-α-galacturonosyltransferase activity | 1.06 (0.04) | – | – |
| At5g06860 | PGIP1 | Polygalacturonase inhibitor activity | 1.53 (0.43) | 4.46 (0.0005) | 1.78 (0.39) |
| At3g04640 | Gly-rich protein | Not assigned | – | 1.13 (0.007) | – |
| At5g67340 | ARM repeat superfamily protein | Ubiquitin-protein ligase activity | – | 1.94 (0.04) | 1.30 (0.52) |
| At5g17760 | P-loop-containing nucleoside triphosphate hydrolases superfamily protein | Nucleoside-triphosphatase activity | – | 2.34 (0.0007) | – |
| At4g37710 | VQ motif-containing protein | Not assigned | – | 2.77 (0.0005) | – |
| AT4G15120 | VQ motif-containing protein | Not assigned | – | 1.36 (0.07) | 1.13 (0.44) |
| At1g08940 | Phosphoglycerate mutase family protein | Catalytic activity | – | 1.28 (0.005) | – |
| At2g26380 | LRR family protein | Not assigned | – | 1.40 (0.002) | – |
| At1g55920 | SAT5 | Ser O-acetyltransferase activity | 1.15 (0.23) | 1.42 (0.03) | – |
| AT2G15490 | UGT73B4 | UDP-glucosyltransferase activity | 1.22 (0.51) | 2.82 (0.006) | – (0.86) |
| At4g24160 | Lysophosphatidic acid acyltransferase | Lysophosphatidic acid acyltransferase activity | 1.62 (0.02) | – | – |
| At2g40000 | HSPRO2 | Not assigned | 1.26 (0.21) | 1.68 (0.02) | 1.18 (0.33) |
| At3g50930 | BCS1 | ATPase activity | 1.88 (0.07) | 2.28 (0.006) | 1.18 (0.45) |
| At2g22880 | VQ motif-containing protein | Not assigned | 1.09 (0.55) | 2.34 (0.01) | 1.30 (0.50) |
| At4g24570 | DIC2 | Dicarboxylic acid transmembrane transporter activity | 2.58 (0.0004) | – | – |
| At1g61340 | F-box family protein | Not assigned | 1.91 (0.0005) | 1.19 (0.007) | – |
| At1g28480 | GRX480 | Protein disulfide oxidoreductase activity | 1.36 (0.37) | 1.44 (0.11) | – |
| At3g17690 | CNGC19 | Ion channel activity (calmodulin binding, cyclic nucleotide binding) | 1.08 (0.29) | 2.32 (0.001) | – |
| At5g64870 | SPFH/band 7/PHB domain-containing membrane-associated protein family | Not assigned | 1.93 (0.0005) | 2.40 (2.83E-05) | – |
| At2g16900 | Phospholipase-like protein (PEARLI4) family | Not assigned | 1.58 (9.00E-05) | 1.18 (0.0006) | – |
| At1g19020 | Unknown protein | Not assigned | 1.36 (0.50) | 1.92 (0.08) | 1.86 (0.34) |
| At1g05575 | Unknown protein | Not assigned | 1.51 (0.23) | 1.16 (0.18) | – |
| At2g28400 | Unknown protein | Not assigned | 1.74 (0.001) | 2.20 (7.30E-05) | – |
| At5g14730 | Unknown protein | Not assigned | 1.35 (0.43) | 1.80 (0.06) | – |
| At4g27652 | Unknown protein | Not assigned | 1.57 (0.03) | – | – |
| At5g65300 | Unknown protein | Not assigned | 1.30 (0.01) | 1.08 (0.01) | – |
| At4g24380 | Unknown protein | Not assigned | 1.39 (0.05) | 2.08 (0.0008) | – |
| At4g29780 | Unknown protein | Not assigned | 1.86 (0.001) | 1.61 (0.001) | – |
| At5g57510 | Unknown protein | Not assigned | – | 2.28 (3.69E-06) | – |
| At1g25400 | Unknown protein | Not assigned | 1.58 (0.03) | 2.53 (0.0003) | – |