Table IV.
Mutant phenotype-associated genes differentially expressed in ntrc relative to Col-0
Fold change values for genes of particular interest are shown in boldface. Values are means of three independent biological replicates. For se values, P values, and a complete list of differentially expressed genes, see Supplemental Table S2. AGI, Arabidopsis Genome Initiative; GO, gene ontology; LD, long day; SD, short day.
| Gene | GO Cellular Component | AGI Code | SD, Seedlings | SD, Leaves | LD, Seedlings | LD, Leaves |
|---|---|---|---|---|---|---|
| fold change | ||||||
| Response to light | ||||||
| CRY2; Cryptochrome 2 | AT1G04400 | 0.36 | 0.46 | 0.39 | 0.47 | |
| FRS3; Far1-related sequence 3 | AT2G27110 | 0.40 | 0.44 | 0.36 | 0.42 | |
| Chloroplast biogenesis + chlorophyll biosynthesis + photosynthesis | ||||||
| FZL; Thylakoid membrane organization-like | Chloroplast | AT1G03160 | 0.30 | 0.38 | 0.33 | 0.46 |
| CLB6; Chloroplast biogenesis 6 | Chloroplast | AT4G34350 | 1.11 | 1.92 | 1.41 | 1.55 |
| GUN5; Genomes uncoupled 5 | Chloroplast | AT5G13630 | 1.15 | 3.32 | 1.24 | 1.72 |
| HEMA1; Glutamyl-tRNA reductase | Chloroplast | AT1G58290 | 0.99 | 2.07 | 1.41 | 1.43 |
| LHCB1B1; PSII light-harvesting complex gene 1.4 | Chloroplast | AT2G34430 | 0.44 | 0.47 | 0.46 | 0.35 |
| LHCB1B2; PSII light-harvesting complex gene 1.5 | Chloroplast | AT2G34420 | 0.44 | 0.47 | 0.51 | 0.35 |
| LHCB2.2; PSII light-harvesting complex gene 2.2 | Chloroplast | AT2G05070 | 0.73 | 0.61 | 0.60 | 0.52 |
| LHCB3; Light-harvesting chlorophyll binding 3 | Chloroplast | AT5G54270 | 0.78 | 0.53 | 1.06 | 0.62 |
| Rubisco small subunit 1A | Chloroplast | AT1G67090 | 0.68 | 0.50 | 0.48 | 0.40 |
| Photorespiration | ||||||
| CAT2; Catalase 2 | Peroxisome | AT4G35090 | 1.09 | 1.90 | 1.09 | 1.35 |
| GGT1; Ala-2-oxoglutarate aminotransferase 1 | Peroxisome | AT1G23310 | 0.98 | 2.20 | 1.18 | 1.57 |
| HPR; Hydroxypyruvate reductase | Peroxisome | AT1G68010 | 1.05 | 2.04 | 1.17 | 1.24 |
| SHM1; Ser hydroxymethyltransferase 1 | Mitochondrion | AT4G37930 | 0.99 | 2.57 | 1.22 | 1.58 |
| CDCP1; Gly decarboxylase P-protein 1 | Mitochondrion | AT4G33010 | 1.00 | 2.21 | 1.08 | 1.31 |
| FdGOGAT; Fd-dependent Glu synthase 1 | Chloroplast | AT5G04140 | 1.21 | 2.81 | 1.16 | 1.63 |
| Proteases | ||||||
| ATPREP1/ATZNMP; Zinc metalloprotease pitrilysin subfamily A | Chloroplast/mitochondrion | AT3G19170 | 1.22 | 2.36 | 1.46 | 1.31 |
| CLPC1; Clp protease, heat shock protein 93-V | Chloroplast | AT5G50920 | 1.00 | 2.31 | 0.95 | 1.38 |
| TPP2; Tripeptidyl peptidase II | Chloroplast | AT4G20850 | 1.32 | 2.17 | 1.52 | 1.70 |
| Metalloendopeptidase | Chloroplast | AT5G42390 | 1.27 | 1.82 | 1.26 | 1.27 |
| Stomatal development | ||||||
| SDD1; Stomatal density and distribution | Secretion | AT1G04110 | 0.47 | 0.62 | 0.40 | 0.53 |
| EPF1; Epidermal patterning factor 1 | Secretion | AT2G20875 | 0.50 | 0.49 | 0.37 | 0.47 |
| Heat shock proteins + stress responses | ||||||
| HSP70; Heat shock protein 70 | AT3G12580 | 1.01 | 3.24 | 1.37 | 1.26 | |
| HSP81-3; Heat shock protein 81-3 | Secretion | AT5G56010 | 1.01 | 2.85 | 1.08 | 1.37 |
| HSP70-3, Heat shock cognate 70-kD protein 3 | AT3G09440 | 0.90 | 2.83 | 1.21 | 1.30 | |
| HSP81-1; Heat shock protein 81-1 | AT5G52640 | 1.41 | 2.20 | 1.44 | 1.39 | |
| HSP17.6-CII; 17.6-kD class II heat shock protein | AT5G12020 | 1.14 | 2.09 | 1.30 | 1.20 | |
| AT-HSP17.6A; Heat shock protein 17.6A | AT5G12030 | 0.91 | 1.86 | 1.12 | 1.14 | |
| BIP; Luminal binding protein | Secretion | AT5G42020 | 1.01 | 2.02 | 1.16 | 1.52 |
| GPX7; Glutathione peroxidase | Chloroplast | AT4G31870 | 1.39 | 1.92 | 1.76 | 1.85 |
| RCD1; Radical-induced cell death 1 | AT1G32230 | 1.23 | 2.11 | 1.31 | 1.38 | |