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. 2006 Sep;142(1):148–167. doi: 10.1104/pp.105.076232

Table I.

Summary of microarray data for A. halleri root and shoot candidate genes

ATH1 probe set identifiers and the corresponding A. thaliana locus identifiers are given for candidate genes more highly expressed in A. halleri than in A. thaliana under control conditions (genes that passed the value filter as described in “Materials and Methods”). In addition, genes were included that showed an at least 2-fold up-regulation or down-regulation upon short-term Zn supply in A. halleri. Raw signal denotes mean signal value calculated from signal values exported from MAS 5.0 using GeneSpring. Microarray data for short-term Zn supply and Zn deficiency are given where the regulation compared to controls was at least 2-fold. One sample Student's t tests were performed in GeneSpring on ratios from cross species and on fold changes from within-species comparisons, P values are indicated as follows: * = P < 0.05; ** = P < 0.01; *** = P < 0.001.

ATH1 Probe Set Identifier AGI Locus Identifier Gene Name A. halleri Raw Signal A. halleri/A. thaliana Signal Ratio A. halleri Fold Change −Zn(II) A. halleri Fold Change +Zn(II), Root: 2 h, Shoot: 8 h A. thaliana Fold Change +Zn(II), Root: 2 h, Shoot: 8 h Annotation
Root Candidates
Cytoplasmic metal influx
    262546_at At1g31260 ZIP10a 141 111** 3.74 ZIP family of metal transporters
    253413_at At4g33020 ZIP9 617 36.2*** ZIP family of metal transporters
    260462_at At1g10970 ZIP4 722 24.6*** 2.29 0.31 ZIP family of metal transporters
    259723_at At1g60960 IRT3a 738 4.47* 2.79 0.28 0.37* ZIP family of metal transporters
    257715_at At3g12750 ZIP1 194 4.08* 2.05 ZIP family of metal transporters
    266336_at At2g32270 ZIP3a 849 1.71* 0.37 0.30* ZIP family of metal transporters
Root-to-shoot metal transport
    258646_at At3g08040 FRD3a 2,890 44.6*** Multidrug and toxin efflux family transporter
Other membrane transport
    266184_s_at At2g38940 PHT1;4a 822 19.1** Phosphate:H+ symporter family, ScPho84 like
    253658_at At4g30120 HMA3 457 9.14* P1B CPX metal ATPase family
    267266_at At2g23150 NRAMP3 685 6.61*** Natural resistance-associated macrophage protein family
    249255_at At5g41610 CHX18a 34.1 6.52* Cation/H+ exchanger of unknown specificity, CPA2 family
    266718_at At2g46800 MTP1 1,561 6.40*** Cation diffusion facilitator family
    267029_at At2g38460 IREG2a 248 4.49*** Similar to human Fe-regulated Fe transporter
Nicotianamine/thiol biosynthesis pathways
    248048_at At5g56080 NAS2 2,765 48.4*** Nicotianamine synthase
    259632_at At1g56430 NAS4b 70.1 13.7 2.42 Nicotianamine synthase
    264261_at At1g09240 NAS3 106 5.22** 3.81* Nicotianamine synthase
    263838_at At2g36880 SAMS3a 5,353 4.31* S-adenosyl-Met synthetase
    250832_at At5g04950 NAS1b 90.1 0.81 Nicotianamine synthase
Other metal handling
    257365_x_at At2g26020 PDF1.2b 57.15 37.2* Plant defensin, antifungal protein AFP5d
Shoot Candidates
Cytoplasmic metal influx
    267304_at At2g30080 ZIP6 288 7.34*** ZIP family of metal transporters
    260462_at At1g10970 ZIP4 256 4.04* 12.70** ZIP family of metal transporters
Root-to-shoot metal transport
    267488_at At2g19110 HMA4a 113 52.5** P1B CPX metal ATPase family
Other membrane transport
    253658_at At4g30120 HMA3 796 358** P1B CPX metal ATPase family
    251620_at At3g58060 MTP8a 108 65.0** Cation diffusion facilitator family
    266718_at At2g46800 MTP1 4,862 27.9*** Cation diffusion facilitator family
    246276_at At4g37270 HMA1 416 12.6** P1B CPX metal ATPase family
    267266_at At2g23150 NRAMP3 309 7.30*** Natural resistance-associated macrophage protein family
    266963_at At2g39450 MTP11a 465 4.74*** Cation diffusion facilitator family
    253339_at At4g33520 HMA6a 148 4.58** P1B CPX metal ATPase family; PAA1
    257789_at At3g27020 YSL6a 256 4.42* 2.54 Yellow-stripe-like transporter family
Nicotianamine/thiol biosynthesis pathways
    256930_at At3g22460 OASA2c 188 10.6*** 2.43 O-acetyl-Ser thiol lyase
    260913_at At1g02500 SAMS1a 988 10.4** 3.68 S-adenosyl-Met synthetase
    255552_at At4g01850 SAMS2a 1,765 8.54*** 2.10 S-adenosyl-Met synthetase
    264261_at At1g09240 NAS3 316 7.89** 5.01* Nicotianamine synthase
    263838_at At2g36880 SAMS3a 2,392 5.31** 2.04 S-adenosyl-Met synthetase
Other metal handling
    256416_at At3g11050 FER2a 83.1 11.0* Ferritin, Fe(III) binding
    257365_x_at At2g26020 PDF1.2b 5,023 7.95* Plant defensin, antifungal protein AFP5d
    251109_at At5g01600 FER1a 6,509 5.13** Ferritin, Fe(III) binding
Stress protection
    262504_at At1g21750 PDI1a 2,538 39.5** 3.76 Protein disulfide isomerase
    259757_at At1g77510 PDI2c 742 17.5** 2.65 Protein disulfide isomerase
a

Newly identified candidate gene.

b

Data for 259632_at, NAS4, and 250832_at, NAS1, in roots are given for comparison.

c

Identified as false positive by real-time RT-PCR (Table II).