Table I.
List of repressed genes in the stop1 mutant among up-regulated or stable genes in the wild type under Al and low-pH conditions (Fig. 1)
Three biologically independent replications of competitive microarray analyses were carried out as follows: stop1 mutant versus the wild type in Al (10 μm, 24 h) or low pH (pH 4.5, 24 h); AtALMT1-KO versus the wild type in Al (10 μm, 24 h); control (pH 5.0, no Al, 24 h) versus Al (10 μm, pH 5.0, 24 h) or low pH (pH 4.5, 24 h) in the wild type. FC ± sd values are shown, as are P values from t tests for significant differences from FC = 1.00.
| Arabidopsis Genome Initiative Code | FC (stop1 Mutant or AtALMT1-KO/Wild Type)
|
FC in the Wild Type with Al or Low-pH Treatments (Treatment/Control)
|
Description | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Al stop1 Mutant
|
Low-pH stop1 Mutant
|
Al AtALMT1-KO
|
Al
|
Low pH
|
|||||||
| FC ± sd | P | FC ± sd | P | FC ± sd | P | FC ± sd | P | FC ± sd | P | ||
| Repressed in the stop1 mutant and up-regulated or stable in the wild type with Al and low-pH treatments; 12 (+1 of the gene repressed in AtALMT1-KO) genes | |||||||||||
| At1g08430 | 0.01 ± 0.00 | 0.001 | 0.01 ± 0.00 | 0.000 | 0.01 ± 0.00 | 0.001 | 24.40 ± 13.8 | 0.009 | 7.41 ± 4.07 | 0.021 | ATALMT1 (Al-activated malate transporter 1) |
| At1g30270 | 0.13 ± 0.03 | 0.003 | 0.19 ± 0.02 | 0.001 | 1.02 ± 0.14 | 0.866 | 1.44 ± 0.09 | 0.009 | 1.42 ± 0.25 | 0.073 | ATCIPK23 (CBL-interacting protein kinase 23) |
| At1g51840 | 0.25 ± 0.06 | 0.010 | 0.40 ± 0.06 | 0.008 | 1.03 ± 0.15 | 0.765 | 1.31 ± 0.42 | 0.272 | 1.21 ± 0.30 | 0.305 | Similar to Leu-rich repeat protein kinase, putative |
| At2g18480 | 0.06 ± 0.01 | 0.002 | 0.12 ± 0.09 | 0.031 | 1.08 ± 0.15 | 0.433 | 6.97 ± 1.12 | 0.002 | 1.89 ± 0.08 | 0.001 | PLT3 (probable polyol transporter 3) |
| At2g41380 | 0.04 ± 0.01 | 0.003 | 0.14 ± 0.08 | 0.025 | 1.11 ± 0.16 | 0.327 | 6.98 ± 3.70 | 0.021 | 2.28 ± 0.57 | 0.028 | Similar to embryo-abundant protein-related |
| At5g02480 | 0.19 ± 0.03 | 0.003 | 0.31 ± 0.08 | 0.015 | 1.07 ± 0.15 | 0.491 | 2.02 ± 0.31 | 0.015 | 1.18 ± 0.07 | 0.040 | Similar to SLT1 (sodium- and lithium-tolerant 1) |
| At5g06860 | 0.05 ± 0.00 | 0.000 | 0.13 ± 0.06 | 0.017 | 1.17 ± 0.17 | 0.201 | 1.93 ± 1.46 | 0.232 | 1.00 ± 0.74 | 0.992 | PGIP1 (polygalacturonase-inhibiting protein 1) |
| At5g18170 | 0.08 ± 0.01 | 0.001 | 0.27 ± 0.11 | 0.030 | 1.26 ± 0.18 | 0.109 | 2.91 ± 0.39 | 0.005 | 1.19 ± 0.10 | 0.068 | GDH1 (glutamate dehydrogenase 1) |
| At5g19600 | 0.01 ± 0.00 | 0.002 | 0.29 ± 0.06 | 0.008 | 1.33 ± 0.19 | 0.074 | 1.50 ± 0.45 | 0.138 | 2.08 ± 0.37 | 0.019 | SULTR3;5 (sulfate transporter 3;5) |
| At5g22890 | 0.06 ± 0.01 | 0.001 | 0.16 ± 0.08 | 0.023 | 1.07 ± 0.15 | 0.520 | 1.03 ± 0.20 | 0.809 | 1.15 ± 0.15 | 0.200 | STOP2 (a STOP1 homolog) |
| At5g38200 | 0.02 ± 0.00 | 0.001 | 0.10 ± 0.04 | 0.009 | 1.06 ± 0.15 | 0.552 | 4.16 ± 1.79 | 0.027 | 1.77 ± 0.19 | 0.012 | Similar to hydrolase |
| At5g66650 | 0.24 ± 0.03 | 0.003 | 0.19 ± 0.13 | 0.043 | 1.03 ± 0.15 | 0.766 | 9.13 ± 1.11 | 0.001 | 2.68 ± 1.17 | 0.055 | Similar to unknown protein |
| At1g53480 | 0.02 ± 0.01 | 0.002 | 0.02 ± 0.01 | 0.007 | 0.01 ± 0.00 | 0.003 | 1.02 ± 0.02 | 0.341 | 1.10 ± 0.05 | 0.060 | Similar to unknown protein |
| Repressed in the stop1 mutant and up-regulated or stable in the wild type with Al treatment; 24 genes | |||||||||||
| At1g35670 | 0.34 ± 0.02 | 0.001 | 0.76 ± 0.06 | 0.030 | 1.05 ± 0.15 | 0.598 | 1.35 ± 0.07 | 0.011 | 0.53 ± 0.08 | 0.020 | ATCDPK2 (calcium-dependent protein kinase 2) |
| At1g60610 | 0.26 ± 0.05 | 0.006 | 0.54 ± 0.05 | 0.008 | 0.95 ± 0.14 | 0.618 | 1.68 ± 0.23 | 0.023 | 1.16 ± 0.10 | 0.095 | Similar to protein-binding/zinc ion-binding |
| At1g61560 | 0.26 ± 0.03 | 0.003 | 0.61 ± 0.09 | 0.029 | 0.99 ± 0.14 | 0.955 | 3.34 ± 0.75 | 0.011 | 2.65 ± 1.02 | 0.045 | MLO6 (mildew resistance locus O6) |
| At1g72870 | 0.22 ± 0.09 | 0.021 | 0.59 ± 0.15 | 0.064 | 0.92 ± 0.13 | 0.406 | 1.29 ± 0.32 | 0.213 | 0.60 ± 0.05 | 0.008 | Putative disease resistance protein (TIR-NBS class) |
| At1g77760 | 0.18 ± 0.05 | 0.008 | 0.88 ± 0.30 | 0.574 | 1.29 ± 0.19 | 0.088 | 1.66 ± 0.30 | 0.038 | 1.68 ± 0.13 | 0.007 | NIA1 (nitrate reductase 1) |
| At2g01180 | 0.31 ± 0.03 | 0.003 | 0.59 ± 0.09 | 0.028 | 1.03 ± 0.15 | 0.779 | 2.13 ± 0.32 | 0.013 | 1.04 ± 0.09 | 0.525 | ATPAP1 (phosphatidic acid phosphatase 1) |
| At2g16660 | 0.34 ± 0.01 | 0.001 | 0.53 ± 0.06 | 0.009 | 1.23 ± 0.18 | 0.126 | 2.62 ± 0.66 | 0.021 | 1.29 ± 0.43 | 0.310 | Similar to nodulin family protein |
| At2g23150 | 0.31 ± 0.03 | 0.002 | 0.61 ± 0.13 | 0.054 | 1.04 ± 0.16 | 0.661 | 2.80 ± 0.55 | 0.012 | 1.27 ± 0.08 | 0.020 | NRAMP3 (manganese ion transporter) |
| At2g28270 | 0.08 ± 0.03 | 0.006 | 0.41 ± 0.26 | 0.114 | 0.98 ± 0.23 | 0.873 | 2.52 ± 0.92 | 0.046 | 0.74 ± 0.34 | 0.357 | Similar to DC1 domain-containing protein |
| At2g39380 | 0.28 ± 0.05 | 0.005 | 0.83 ± 0.07 | 0.064 | 1.03 ± 0.15 | 0.753 | 1.41 ± 0.21 | 0.054 | 2.63 ± 0.22 | 0.003 | ATEXO70H2 (exocyst subunit EXO70 family protein H2) |
| At2g39510 | 0.27 ± 0.07 | 0.013 | 1.32 ± 1.12 | 0.579 | 1.35 ± 0.20 | 0.072 | 9.60 ± 7.83 | 0.032 | 1.97 ± 1.57 | 0.235 | Similar to nodulin MtN21 family protein |
| At2g43590 | 0.25 ± 0.10 | 0.025 | 1.09 ± 0.50 | 0.754 | 0.84 ± 0.15 | 0.157 | 3.20 ± 0.63 | 0.009 | 2.22 ± 2.00 | 0.214 | Putative chitinase |
| At2g45220 | 0.26 ± 0.04 | 0.005 | 0.69 ± 0.02 | 0.003 | 1.13 ± 0.29 | 0.458 | 1.98 ± 0.26 | 0.012 | 0.43 ± 0.11 | 0.026 | Similar to pectin esterase family protein |
| At3g05400 | 0.19 ± 0.04 | 0.004 | 0.63 ± 0.15 | 0.076 | 1.20 ± 0.17 | 0.158 | 2.98 ± 1.04 | 0.031 | 1.07 ± 0.09 | 0.293 | SUGTL5 (sugar transporter ERD6-like 12) |
| At3g28290 | 0.13 ± 0.03 | 0.004 | 0.46 ± 0.16 | 0.055 | 0.87 ± 0.12 | 0.237 | 1.51 ± 0.13 | 0.014 | 0.93 ± 0.28 | 0.713 | Similar to AT14A |
| At4g13420 | 0.03 ± 0.00 | 0.000 | 2.21 ± 1.35 | 0.135 | 0.84 ± 0.12 | 0.165 | 7.54 ± 4.39 | 0.023 | 6.86 ± 1.12 | 0.002 | HAK5 (high-affinity K+ transporter 5) |
| At4g16563 | 0.09 ± 0.07 | 0.026 | 0.22 ± 0.27 | 0.113 | 1.13 ± 0.28 | 0.449 | 1.22 ± 0.31 | 0.307 | 0.35 ± 0.04 | 0.004 | Similar to aspartyl protease family protein |
| At4g30270 | 0.28 ± 0.06 | 0.010 | 0.84 ± 0.63 | 0.693 | 0.91 ± 0.15 | 0.407 | 12.56 ± 5.39 | 0.009 | 2.05 ± 0.76 | 0.074 | MERI5B (endoxyloglucan transferase) |
| At4g38470 | 0.29 ± 0.05 | 0.007 | 0.80 ± 0.22 | 0.297 | 1.17 ± 0.17 | 0.200 | 1.13 ± 0.20 | 0.343 | 1.15 ± 0.17 | 0.245 | Similar to protein kinase family protein |
| At5g07440 | 0.29 ± 0.05 | 0.005 | 0.54 ± 0.15 | 0.060 | 1.16 ± 0.17 | 0.208 | 2.55 ± 0.16 | 0.001 | 1.23 ± 0.17 | 0.123 | GDH2 (glutamate dehydrogenase 2) |
| At5g11670 | 0.26 ± 0.07 | 0.012 | 0.67 ± 0.06 | 0.017 | 1.02 ± 0.14 | 0.834 | 3.62 ± 0.78 | 0.009 | 1.53 ± 0.15 | 0.018 | ATNADP-ME2 (malic enzyme 2) |
| At5g17860 | 0.31 ± 0.03 | 0.003 | 0.98 ± 0.02 | 0.208 | 0.98 ± 0.17 | 0.837 | 1.28 ± 0.06 | 0.012 | 1.02 ± 0.06 | 0.681 | CAX7 (calcium exchanger 7) |
| At5g47560 | 0.12 ± 0.02 | 0.002 | 0.75 ± 0.15 | 0.129 | 1.09 ± 0.19 | 0.423 | 1.05 ± 0.12 | 0.557 | 1.06 ± 0.12 | 0.457 | ATTDT (tonoplast malate/fumarate transporter) |
| At5g66800 | 0.33 ± 0.03 | 0.003 | 0.58 ± 0.06 | 0.011 | 0.71 ± 0.11 | 0.057 | 1.04 ± 0.05 | 0.248 | 0.91 ± 0.06 | 0.124 | Similar to unknown protein |
| Repressed in the stop1 mutant and up-regulated or stable in the wild type with low-pH treatment; four genes | |||||||||||
| At1g62280 | 0.97 ± 0.62 | 0.936 | 0.47 ± 0.01 | 0.001 | 0.84 ± 0.15 | 0.161 | 0.33 ± 0.30 | 0.133 | 1.06 ± 0.51 | 0.858 | SLAH1 (SLAC1 homolog 1) |
| At1g75840 | 0.58 ± 0.04 | 0.005 | 0.47 ± 0.03 | 0.002 | 0.99 ± 0.15 | 0.879 | 0.94 ± 0.14 | 0.570 | 1.03 ± 0.06 | 0.460 | ATROP4 (rho-like GTP-binding protein 4) |
| At3g12750 | 0.60 ± 0.05 | 0.010 | 0.46 ± 0.09 | 0.020 | 1.42 ± 0.21 | 0.053 | 0.55 ± 0.04 | 0.004 | 1.62 ± 0.13 | 0.009 | ZIP1 (zinc transporter 1) |
| At5g24780 | 0.65 ± 0.57 | 0.431 | 0.43 ± 0.01 | 0.000 | 2.21 ± 0.42 | 0.004 | 1.06 ± 1.02 | 0.918 | 4.00 ± 1.69 | 0.027 | VSP1 (vegetative storage protein1) |