Table III. Genes comprising RM2.
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/Process | Fold (Log2) |
||
| 1 h | 6 h | 24 h | |||
| At1g12560a,b,c | EXP7 | Plant-type cell wall loosening | 1.83 (0.29) | 1.35 (0.25) | 1.24 (0.65) |
| At2g03720a,b,c | MRH6 | Root hair cell differentiation | 1.00 (0.58) | 1.45 (0.11) | 1.30 (0.48) |
| At1g05650/At1g05660 | Polygalacturonase/pectinase, putative | Polygalacturonase activity | 1.44 (0.07) | 2.43 (0.0005) | 1.72 (0.56) |
| At3g18200 | Nodulin MtN21 family protein | Not assigned | 1.09 (0.08) | 1.51 (0.003) | – |
| At3g12540a,b,c | Unknown protein | Not assigned | 1.28 (0.13) | – | 1.02 (0.37) |
| At3g58000a,b | VQ motif-containing protein | Not assigned | 1.83 (0.20) | −2.05 (0.04) | −1.15 (0.62) |
| At4g25790a,b,c | CAP superfamily protein | Not assigned | 1.26 (0.51) | −1.68 (0.10) | – |
| At4g30320a,b | CAP superfamily protein | Not assigned | 1.32 (0.54) | −1.90 (0.09) | −1.22 (0.66) |
| At5g14340 | MYB40 | Sequence-specific DNA-binding transcription factor activity | 1.14 (0.03) | – | – |
| At5g43230a,b | Unknown protein | Not assigned | 1.04 (1.00) | – | – |
| At4g29180a,b,c | RHS16 | Kinase activity | – | −1.00 (0.06) | – |
| At1g63450a,c | RHS8 | Not assigned | – | −1.69 (0.005) | −1.49 (0.09) |
| At2g45890a,c | RHS11, ROPGEF4 | Rho guanyl nucleotide-exchange factor activity | – | – | −1.08 (0.32) |
| At2g21880a,b | ATRAB7A | GTP binding | – | −2.01 (0.004) | −1.51 (0.14) |
| At3g07070a,b,c | Protein kinase family protein | Protein Ser/Thr kinase activity | – | −1.04 (0.11) | – |
| At4g03330a,b,c | SYP123 | SNAP receptor activity | – | −1.09 (0.08) | – |
| At3g43960a | Cys proteinase | Cys-type endopeptidase activity | – | −1.44 (0.03) | – |
| At5g15600 | SP1L4 | Not assigned | – | −1.33 (0.04) | – |
| At3g54770 | RNA-binding (RRM/RBD/RNP motifs) family protein | RNA binding | – | −2.42 (0.002) | −1.04 (0.46) |
| At5g24100 | LRR transmembrane protein kinase | Protein amino acid phosphorylation | – | −1.37 (0.004) | −1.08 (0.12) |
| At3g63470 | SCPL40 | Ser-type carboxypeptidase activity | – | −1.50 (0.002) | – |
| At4g33790 | CER4 | Fatty acyl-CoA reductase (alcohol-forming) activity | – | −2.17 (0.0002) | −1.44 (0.03) |
| At2g25240b | Ser protease inhibitor | Ser-type endopeptidase inhibitor activity | – | – | −1.14 (0.37) |
| At3g56230b | Speckle-type POZ protein related | Not assigned | – | – | −1.40 (0.22) |
| At1g24620 | EF-hand calcium-binding protein family | Calcium ion binding | – | −1.51 (0.02) | −1.36 (0.19) |
| At1g53680a,b,c | ATGSTU28 | Glutathione transferase activity | – | −1.68 (0.02) | −1.25 (0.33) |
| At2g19060a | SGNH hydrolase-type esterase superfamily protein | Hydrolase activity | – | – | −1.03 (0.37) |
| At2g25680 | MOT1 | Molybdate ion transmembrane transporter activity, sulfate transmembrane transporter activity | – | −1.47 (0.22) | −2.04 (0.31) |
| At3g01730a,b | Unknown protein | Not assigned | – | −1.18 (0.02) | – |
| At3g18450a,b | Unknown protein | Not assigned | – | −2.55 (0.007) | −1.87 (0.21) |
| At3g29110 | Terpenoid cyclase/protein prenyltransferase superfamily protein | Lyase activity | – | −1.80 (0.03) | −1.42 (0.32) |
| At4g08620a,b | SULTR1;1 | Sulfate transmembrane transporter activity | – | −1.50 (0.08) | −2.04 (0.12) |
| At4g12510/At4g12520 | Bifunctional inhibitor/lipid transfer protein/seed storage 2S albumin superfamily protein | Lipid binding | – | −4.81 (0.0005) | −1.93 (0.38) |
| At4g15290 | ATCSLB5 | Cellulose synthase activity | – | −1.22 (0.18) | −1.56 (0.32) |
| At4g20450a,b | LRR protein kinase family protein | Kinase activity | – | −1.21 (0.09) | −1.15 (0.38) |
| At4g22460a,b | Bifunctional inhibitor/lipid transfer protein/seed storage 2S albumin superfamily protein | Lipid binding | – | −2.88 (0.001) | −2.12 (0.08) |
| At4g26320 | AGP13 | Not assigned | – | −3.72 (1.00E-05) | −1.63 (0.07) |
| At5g56540 | AGP14 | Not assigned | – | −1.90 (2.79E-05) | −1.04 (0.03) |
| At5g53250 | AGP22 | Not assigned | – | −3.26 (7.94E-05) | −1.24 (0.26) |
| At4g31470 | CAP superfamily protein | Not assigned | – | −1.16 (0.008) | – |
| At5g04960a,b,c | Plant invertase/pectin methylesterase inhibitor superfamily | Enzyme inhibitor activity, pectinesterase activity | – | −1.62 (0.21) | −1.43 (0.62) |
| At5g19800a,c | Hyp-rich glycoprotein family protein | Not assigned | – | −1.39 (0.09) | – |
| At5g60660 | PIP2;4 | Water channel activity | – | −1.37 (0.31) | −2.46 (0.24) |
| At5g51310a,b | 2-Oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein | Oxidoreductase activity, iron ion binding | – | −1.11 (0.008) | – |
| At5g52350 | ATEXO70A3 | Exocytosis | – | −1.43 (0.06) | −1.05 (0.52) |
| At5g15890a,c | TBL21 | Not assigned | – | – | −1.15 (0.20) |
| At1g12080 | Vacuolar calcium-binding protein related | Not assigned | – | – | −1.11 (0.16) |
| At3g59370a,b | Vacuolar calcium-binding protein related | Not assigned | – | −2.96 (0.001) | −1.71 (0.23) |
| At4g01140 | Unknown protein | Not assigned | – | −1.71 (0.04) | −1.25 (0.43) |
| At1g33900 | P-loop-containing nucleoside triphosphate hydrolase superfamily protein | GTP binding | – | −1.54 (0.002) | −1.37 (0.03) |
a
Genes with root hair-specific cis-regulatory elements (Won et al., 2009).
b
Genes listed in the root hair elongation transcriptome (Jones et al., 2006).
c
Genes that have been attributed to root hair differentiation by bioinformatic approaches (Breen and Grierson, 2007).