Table 2.
Core and common set of root Fe deficiency upregulated genes from Arabidopsis thaliana ecotypes (Tsu-1, Kas-1, Ler, Col-0 and C24). Fold change for −Fe as compared to +Fe is provided when available in original reference, otherwise ‘up’ indicates upregulation in −Fe as compared to +Fe, and ‘down’ indicates downregulated in −Fe as compared to +Fe.
| Fold change (−F versus +Fe) |
|||||||||||||||
| Gene locus | Description | Tsu-1 24 h | Tsu-1 48 h | Kas-1 24 h | Kas-1 48 h | Ler 24 ha | Col-0 24 hb | Col-0 24 hc | Col-0 24 h d | Col-0 48 h d | Col-0 72 h d | Col-0 72 h e | Col-0 72 h f | C24 72 h f | Col-0 g |
| Core set of root upregulated genes (observed in five of five ecotypes) | |||||||||||||||
| At4g19690 | IRT1, metal transporter | 3.8 | 6.3 | 29.3 | 61.7 | Up | 27.4 | 29.3 | Up | Up | Up | 16.3 | 13.7 | 6.6 | |
| At4g16370 | OPT3, metal transporter | 1.7 | 5.2 | −1.6 | 1.7 | Up | 5.2 | Up | Up | Up | 7.3 | 5.7 | |||
| At1g23020 | FRO3, metal transporter | 2.8 | 5.4 | 2.0 | 2.8 | Up | 4.8 | Up | Up | Up | 7.8 | 6.7 | |||
| At3g58810 | MTP3/MTPa2, metal transporter | 3.4 | 7.1 | 3.4 | 6.5 | Up | 4.8 | 5.4 | Up | Up | Up | 11.9 | 9.4 | 6.7 | Up |
| At3g56980 | bHLH039, transcription factor | 5.4 | 10.2 | 2.6 | Up | 9.5 | Up | Up | Up | 24.5 | 20.3 | Up | |||
| At3g12900 | 2OG-Fe(II) oxygenase family protein | 2.4 | 9.7 | 6.0 | 19.2 | Up | 24.9 | 11.2 | Up | Up | Up | 18.5 | 95.5 | 35.3 | |
| At3g07720 | Galactose oxidase/kelch repeat-containing protein | 1.6 | 10.5 | 4.2 | 4.0 | Up | 8.3 | 11.2 | Up | Up | Up | 12.9 | 11.3 | 12.1 | Up |
| At5g53450 | ORG1, OBP3 responsive gene (protein kinase) | 1.7 | 3.4 | 2.4 | Up | 4.4 | Up | Up | Up | 5.3 | 3.5 | ||||
| At1g47400 | Unknown protein | 3.0 | 5.2 | 2.7 | 5.9 | Up | 5.2 | Up | Up | Up | 13.6 | 6.6 | |||
| At1g74770 | Unknown protein | 2.0 | 3.7 | 2.4 | Up | Up | Up | 5.4 | 4.9 | ||||||
| Common set of root upregulated genes (observed in four of five ecotypes) | |||||||||||||||
| At4g19680 | IRT2, metal transporter | 4.3 | 5.6 | Up | 3.0 | 3.8 | 21.0 | 14.3 | 7.1 | Up | |||||
| At5g67330 | NRAMP4, metal transporter | 3.0 | Up | 2.0 | Up | Up | Up | 2.2 | 2.0 | ||||||
| At3g58060 | MTPc3, metal transporter | 3.5 | 3.9 | Up | 3.0 | Up | Up | Up | 8.9 | 21.2 | 22.4 | ||||
| At5g02780 | Glutathione S-transferase (flavonoid synthesis) | 3.7 | 7.7 | 3.8 | 7.4 | 7.0 | 11.2 | Up | Up | Up | 19.1 | 27.4 | 21.6 | ||
| At3g50740 | UGT72E1, UDPG:coniferyl alcohol glucosyltransferase | 2.4 | 3.6 | 4.0 | 4.7 | 2.6 | Up | Up | Up | 8.6 | 4.2 | 3.9 | Up | ||
| At1g09560 | GLP5 germin-like protein | 2.3 | 3.7 | Up | 3.8 | 3.0 | Up | Up | Up | 3.0 | 2.4 | ||||
| At1g34760 | GRF11/GR14, 14-3-3 protein, binds H+-ATPase (root hairs) | 2.0 | 2.9 | Up | 2.3 | 3.7 | Up | Up | Up | 18.4 | 9.4 | 10.9 | |||
| At3g06890 | Similar to oxidoreductase/transition metal ion binding | 1.7 | Up | 2.7 | Up | Up | 2.8 | 3.7 | 4.6 | ||||||
| At3g47640 | PYE, bHLH transcription factor | 1.9 | Up | 1.5 | Up | Up | Up | 2.6 | 2.2 | ||||||
| At3g18290 | BTS, E3 ligase | 1.6 | 2.7 | Up | 2.2 | Up | Up | Up | 2.7 | 2.5 | |||||
| At2g20030 | RING-H2 finger protein ATL2D precursor | 1.6 | Up | 2.0 | 3.0 | 3.0 | 2.5 | ||||||||
| At5g05250 | Unknown protein | 2.5 | 7.2 | Up | 3.0 | Up | Up | Up | 6.0 | 4.4 | |||||
| At3g56360 | Unknown protein | 2.2 | 1.6 | Up | 2.7 | Up | Up | Up | 2.3 | 1.6 | |||||
| At1g49000 | Unknown protein | 3.3 | −1.5 | 1.5 | 1.9 | 2.7 | Up | Up | 5.8 | 3.4 | |||||
| At2g29995 | Unknown protein | 1.6 | 1.8 | Up | 2.3 | 3.3 | |||||||||
| At3g61930 | Unknown protein | 3.3 | 8.7 | Up | 11.8 | 6.9 | Up | Up | Up | 32.5 | 23.9 | 11.7 | |||
| Common Set of root upregulated genes (observed in three of five ecotypes) | |||||||||||||||
| At4g30120 | HMA3, P1B-type Zn-ATPase | 1.7 | 1.6 | Up | 5.5 | 5.1 | 4.3 | ||||||||
| At1g80830 | NRAMP1, metal transporter | 1.5 | 4.2 | 2.8 | |||||||||||
| At5g13740 | ZIF1, zinc transporter | Up | 2.5 | Up | Up | Up | 2.6 | 2.3 | |||||||
| At3g46900 | COPT2, Cu transporter | Up | 3.7 | 4.0 | Up | Up | Up | 5.8 | 15.4 | 7.5 | |||||
| At5g03570 | FPN2/IREG2, metal transporter | Up | 3.0 | Up | Up | Up | 6.6 | 6.4 | 4.2 | ||||||
| At5g26820 | IREG3, transporter | Up | Up | 2.3 | 1.9 | ||||||||||
| At5g38820 | Amino acid transporter family protein | 1.7 | 3.3 | Up | 3.7 | 4.5 | Up | Up | Up | 6.8 | 16.3 | ||||
| At3g60330 | AHA7, H+-ATPase | 1.7 | 2.0 | 2.1 | 3.0 | 2.6 | 2.8 | ||||||||
| At5g07390 | RBOHA | 2.6 | Up | Up | 2.3 | 1.6 | |||||||||
| At5g47910 | RBOHD | 1.5 | 2.7 | 2.9 | Up | Up | Up | 3.8 | 4.2 | 4.4 | |||||
| At3g12820 | MYB10, transcription factor | Up | 3.5 | 2.6 | Up | Up | Up | 11.7 | 24.0 | 24.2 | |||||
| At1g56160 | MYB72, transcription factor | Up | 2.2 | 3.4 | Up | Up | Up | 23.4 | 84.5 | 72.2 | |||||
| At2g28160 | FIT, transcription factor | Up | 2.8 | 3.5 | 2.4 | 2.8 | |||||||||
| At5g04150 | bHLH101, transcription factor | Up | 4.1 | Up | Up | Up | 13.9 | 6.1 | |||||||
| At4g01250 | WRKY22, transcription factor | 1.6 | 2.2 | 2.0 | 1.6 | 2.0 | |||||||||
| At2g14210 | MADS box gene, transcription factor | 2.0 | 2.0 | 2.7 | 2.8 | ||||||||||
| At1g02500 | SAM1, S-adenosylmethionine synthetase | 1.8 | 2.1 | Up | Up | Up | 2.6 | 2.2 | |||||||
| At5g04950 | NAS1, nicotianamine synthase | 1.9 | 2.2 | 7.5 | 5.9 | Up | Up | Up | 3.5 | 3.1 | 3.1 | ||||
| At5g13910 | LFY, ethylene response factor subfamily B-1 | 1.8 | Up | Up | 3.1 | 3.7 | |||||||||
| At2g45400 | BEN1, dihydroflavinol 4-reductase-like protein | Up | 2.3 | Up | 2.7 | 3.3 | |||||||||
| At1g14185 | Glucose-methanol-choline (GMC) oxidoreductase family protein | 2.6 | 2.1 | 9.9 | 7.1 | ||||||||||
| At2g16060 | HB1/GLB1, nonsymbiotic haemoglobin | 15.9 | 6.2 | 2.4 | Up | Up | |||||||||
| At5g61250 | Heparanase-like protein 2 | 1.7 | 1.8 | Up | 2.6 | 2.2 | |||||||||
| At4g36010 | Pathogenesis-related thaumatin family protein | 2.6 | 2.0 | 1.8 | Up | Up | |||||||||
| At5g16570 | GLN1, glutamine synthetase | 1.7 | Up | 2.4 | 2.0 | ||||||||||
| At5g36890 | Glycosyl hydrolase family 1 protein | 1.6 | 3.4 | 4.1 | Up | Up | Up | 6.2 | 8.7 | 5.7 | |||||
| At4g17260 | Lactate/malate dehydrogenase family protein | 6.3 | 1.6 | 1.5 | Up | Up | |||||||||
| At2g46710 | rac GTPase activating protein family | 2.5 | 2.2 | 2.1 | |||||||||||
| At3g21240 | Isoform of 4-coumarate:CoA ligase (4CL) | 1.8 | 2.2 | Up | Up | Up | 3.0 | 3.9 | 3.7 | ||||||
| At2g42750 | 4Fe-4S ferredoxin, iron-sulphur-binding family | 1.7 | Up | 1.8 | Up | Up | Up | ||||||||
| At4g30490 | AFG1-like ATPase family protein | 1.5 | 1.7 | 3.3 | 2.5 | ||||||||||
| At4g10510 | Subtilase family protein | 1.7 | Up | Up | 2.1 | 6.2 | 4.8 | ||||||||
| At4g12910 | Serine carboxypeptidase family | −1.5 | 1.6 | Up | Up | 2.3 | 2.4 | 2.1 | |||||||
| At1g18910 | Zinc finger (C3HC4-type RING finger) family protein | Up | 1.7 | Up | Up | 2.8 | 3.2 | 3.0 | |||||||
| At3g53280 | CYP71B5, cytochrome P450 monooxygenase | Up | 3.5 | Up | Up | 19.4 | 40.1 | 33.8 | |||||||
| At3g61410 | U-box domain-containing protein kinase | Up | 2.1 | Up | Up | 3.6 | 4.2 | 4.8 | |||||||
| At4g29220 | PFK1, phosphofructokinase family protein | Up | 1.9 | Up | Up | 2.7 | 2.5 | 2.8 | |||||||
| At4g38950 | Similar to microtubule motor; similar to kinesin heavy chain | −1.5 | Up | 2.1 | 2.0 | 2.1 | |||||||||
| At4g19160 | Unknown protein | 1.5 | Up | Up | 3.3 | 2.6 | |||||||||
| At5g55620 | Unknown protein | Up | 2.1 | Up | Up | 11.6 | 12.3 | ||||||||
| At5g67370 | Unknown protein | Up | 2.6 | Up | Up | Up | 7.3 | 13.3 | |||||||
| At1g01570 | Similar to fringe-related protein | Up | 2.9 | 3.3 | |||||||||||