Table 1.
Copper Deficiency Impacts Various Metabolic Processes
| Process | Gene | Defline | CRR1 ─Cua | CRR1 +Cua | Fold Change | crr1:CRR1 ─Cua | crr1 ─Cua | Fold Change | CRR1 Target | Domain |
| Anaerobic metabolism | FDX5 | Apoferrodoxin | 2742 | 14 | 196 | 1605 | 1 | 1791 | Y | Redox |
| HYDEF | Fe hydrogenase assembly protein | 32 | 2.3 | 14 | 28 | 15 | 1.9 | N | Redox | |
| HYDG | Hydrogenase assembly factor | 79 | 11 | 7.2 | 136 | 127 | N | Redox | ||
| HCP3 | Hybrid cluster protein | 11 | 2.1 | 5.5 | 29 | 23 | 1.3 | N | Redox | |
| PFR1 | Pyruvate-ferredoxin oxidoreductase | 77 | 14 | 5.6 | 41 | 31 | 1.3 | N | Redox | |
| HYD1 | Fe hydrogenase | 184 | 44 | 4.2 | 676 | 146 | 4.6 | N | Redox | |
| 166317 | Prolyl 4-hydroxylase, α-subunit | 104 | 3.2 | 32 | 184 | 16 | 11 | Y | Redox | |
| 114525 | Prolyl 4-hydroxylase, α-subunit | 295 | 38 | 7.8 | 198 | 33 | 6.0 | Y | Redox | |
| 143800 | Prolyl 4-hydroxylase | 57 | 1.6 | 36 | 39 | 1.3 | 30 | Y | Redox | |
| HCP2 | Hybrid-cluster protein | 11 | 5.0 | 2.2 | 38 | 240 | 0.16 | N | Redox | |
| PAT1b | Phosphate acetyltransferase | 30 | 16 | 1.9 | 0.08 | 1.1 | N | |||
| Oxygen-dependent enzymes | 96954 | Prolyl 4-hydroxylase | 118 | 1.4 | 85 | 68 | 5.6 | 12 | Y | Redox |
| 143800 | Prolyl 4-hydroxylase | 57 | 1.6 | 36 | 39 | 1.3 | 30 | Y | Redox | |
| 166317 | Prolyl 4-hydroxylase, α-subunit | 104 | 3.2 | 32 | 184 | 16 | 11 | Y | Redox | |
| 114525 | Prolyl 4-hydroxylase, α-subunit | 295 | 38 | 7.8 | 198 | 33 | 6.0 | Y | Redox | |
| 193036 | Putative glyoxal or galactose oxidase | 528 | 10 | 54 | 430 | 15 | 30 | Y | Redox | |
| GOX17 | Glyoxal or galactose oxidase | 354 | 7.3 | 48 | 294 | 10 | 29 | Y | Redox | |
| GOX7 | Glyoxal or galactose oxidase | 37 | 1.3 | 28 | 26 | 1.6 | 17 | Y | Redox | |
| GOX8c | Glyoxal or galactose oxidase | 8.6 | 0.37 | 23 | 17 | 1.0 | 16 | Y | ||
| GOX3 | Glyoxal or galactose oxidase | 20 | 9.0 | 2.2 | 16 | 7.7 | 2.0 | Y | Redox | |
| HPD1 | 4-Hydroxyphenylpyruvate dioxygenase | 114 | 2.5 | 45 | 32 | 14 | 2.3 | Y | Redox | |
| CPX1 | Coproporphyrinogen III oxidase | 3483 | 232 | 15 | 1109 | 166 | 6.7 | Y | Redox | |
| CRD1 | Copper response defect 1 protein | 2047 | 176 | 12 | 1168 | 89 | 13 | Y | Redox | |
| CAO | Chlorophyll a oxygenase | 254 | 99 | 2.6 | 177 | 107 | 1.7 | N | Redox | |
| 113197 | Prolyl 4-hydroxylase, α-subunit | 18 | 7.8 | 2.3 | 6.3 | 6.5 | N | Redox | ||
| CDO1 | Cysteine dioxygenase | 14 | 6.2 | 2.2 | 9.5 | 12 | N | Redox | ||
| Lipid metabolism | CYP51G1 | Sterol 14 desaturase | 249 | 50 | 5.0 | 84 | 31 | 2.8 | Y | Redox |
| CYP745A1 | Cytochrome P450 | 120 | 24 | 4.9 | 57 | 18 | 3.3 | Y | Redox | |
| 59933 | SC5D, C-5 sterol desaturase | 189 | 41 | 4.6 | 77 | 30 | 2.6 | Y | Redox | |
| FAB2 | Plastid acyl-ACP desaturase | 866 | 187 | 4.6 | 592 | 121 | 4.9 | Y | Redox | |
| CYP710B1 | Cytochrome P450, C-22 desaturase | 177 | 52 | 3.4 | 175 | 46 | 3.8 | Y | Redox | |
| FAD5A | MGDG-specific palmitate Δ-7 desaturase | 285 | 97 | 2.9 | 142 | 40 | 3.5 | Y | Redox | |
| DES6 | ω-6-FAD, chloroplast isoform | 4029 | 1758 | 2.3 | 1538 | 2315 | 0.66 | N | Redox | |
| 135825 | Fatty acid desaturase, Δ-12 | 57 | 22 | 2.6 | 24 | 17 | 1.4 | N | Redox | |
| 40101 | Acyl-CoA dehydrogenase | 80 | 33 | 2.4 | 25 | 14 | 1.9 | N | Redox | |
| 177689 | CDP-alcohol phosphatidyltransferase | 29 | 10 | 3.0 | 11 | 9.4 | N | Other | ||
| CYP747A1 | Cytochrome P450 | 15 | 6.3 | 2.4 | 13 | 11 | N | Redox | ||
| SMT1 | Sterol-C24-methyltransferase | 474 | 232 | 2.0 | 264 | 146 | 1.8 | N | Other | |
| Copper assimilation | CTR1 | CTR-type copper ion transporter | 60 | 18 | 3.4 | 59 | 5.6 | 10 | Y | Transport |
| CTR2 | CTR-type copper ion transporter | 171 | 8.6 | 20 | 101 | 0.86 | 118 | Y | Transport | |
| CTR3 | CTR-type copper ion transporter | 209 | 19 | 11 | 269 | 8 | 34 | Y | Transport | |
| IRT2 | ZIP family transporter | 20 | 0.94 | 21 | 53 | 7.0 | 7.7 | Y | Transport | |
| Fe assimilation | FEA1 | Fe-assimilating protein | 448 | 226 | 2.0 | 3010 | 1760 | 1.7 | N | Other |
| Copper backup enzyme | AOF1 | Amine oxidase-like protein | 67 | 17 | 3.9 | 11 | 5.0 | 2.2 | Y | Redox |
| Chloroplastmetabolism | CYC6 | Cytochrome c6 | 2677 | 0.81 | 3315 | 1589 | 1.1 | 1427 | Y | Redox |
| FDX5 | Apoferrodoxin | 2742 | 14 | 196 | 1605 | 0.90 | 1791 | Y | Redox | |
| CGL78 | Conserved green lineage | 1514 | 194 | 7.8 | 699 | 78 | 9.0 | Y | Unknown | |
| FDX6 | Apoferrodoxin | 69 | 155 | 2.3 | 227 | 80 | 2.8 | Y | Redox |
The genes involved in anaerobic metabolism were identified previously (Mus et al., 2007). Genes without functional annotation in the FM3.1 set of Chlamydomonas gene models are indicated with a protein ID. To determine if the expression of genes is CRR1 dependent, the mRNA transcript abundances in crr1 and crr1:CRR1 cells were considered. A fold difference ≥ 2.0 with an FDR < 0.05 was considered significant, and the corresponding gene was considered a CRR1 target. The predicted domain function was determined via Pfam (E-value ≤1 × 10−4).
a
Transcript abundance, RPKM.
b
Transcript with fold change <2; not included in Supplemental Data Set 3 online.
c
Transcript abundance is <10; not included in Supplemental Data Set 3 online; verified fold change via RT-PCR.