Skip to main content

Main menu

  • For Authors
    • Submit a Manuscript
    • Instructions for Authors
  • Home
  • Content
    • Current Issue
    • Archive
    • Preview Papers
    • Focus Collections
    • Classics Collection
    • Upcoming Focus Issues
  • Advertisers
  • About
    • About the Journal
    • Editorial Board and Staff
  • Subscribers
  • Librarians
  • More
    • Alerts
    • Contact Us
  • Other Publications
    • Plant Physiology
    • The Plant Cell
    • Plant Direct
    • The Arabidopsis Book
    • Plant Cell Teaching Tools
    • ASPB
    • Plantae

User menu

  • My alerts
  • Log in

Search

  • Advanced search
Plant Physiology
  • Other Publications
    • Plant Physiology
    • The Plant Cell
    • Plant Direct
    • The Arabidopsis Book
    • Plant Cell Teaching Tools
    • ASPB
    • Plantae
  • My alerts
  • Log in
Plant Physiology

Advanced Search

  • For Authors
    • Submit a Manuscript
    • Instructions for Authors
  • Home
  • Content
    • Current Issue
    • Archive
    • Preview Papers
    • Focus Collections
    • Classics Collection
    • Upcoming Focus Issues
  • Advertisers
  • About
    • About the Journal
    • Editorial Board and Staff
  • Subscribers
  • Librarians
  • More
    • Alerts
    • Contact Us
  • Follow plantphysiol on Twitter
  • Visit plantphysiol on Facebook
  • Visit Plantae
Research ArticleRESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS
You have accessRestricted Access

Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants

John P. Hammond, Malcolm J. Bennett, Helen C. Bowen, Martin R. Broadley, Dan C. Eastwood, Sean T. May, Clive Rahn, Ranjan Swarup, Kathryn E. Woolaway, Philip J. White
John P. Hammond
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Malcolm J. Bennett
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Helen C. Bowen
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martin R. Broadley
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dan C. Eastwood
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sean T. May
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Clive Rahn
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ranjan Swarup
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kathryn E. Woolaway
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Philip J. White
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site

Published June 2003. DOI: https://doi.org/10.1104/pp.103.020941

  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Figure 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 1.

    The effect of P withdrawal on shoot fresh weight (A) and shoot P concentration expressed on a dry weight basis (B). Arabidopsis plants were grown hydroponically in a complete nutrient solution (•) or a solution lacking P (○). Plants were 28 d old at the beginning of the experiment. Data are expressed as mean ± SE (n = 3 experiments).

  • Figure 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 2.

    Venn diagrams showing the numbers of genes differentially expressed in shoots of Arabidopsis plants in response to 4, 28, and 100 h of P starvation (A); 28 + 4 h of P starvation (late P-responsive genes), 28 h of K starvation, and 28 h N starvation (B); 4 h of P starvation (early P-responsive genes), 28 h of K starvation, and 28 h of N starvation (C). Differentially expressed genes were defined as those with a -fold difference in expression in two biological replicates of 2.5 between shoots of plants grown in solutions lacking specific elements and control plants grown in complete nutrient solutions and harvested at the same growth stage. The identities of genes that were differentially expressed in response to P, K, or N starvation are given in Tables I and II.

  • Figure 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 3.

    The MIPS functional categories of genes whose expression had changed early (4 h; Table I) or late (28 or 100 h; Table II) after the withdrawal of P from 28-d-old hydroponically grown Arabidopsis. The AGI number for each gene was used to identify its functional category from the MIPS database (http://mips.gsf.de/proj/thal/db/tables/tables_func_frame.html). When no functional category was given by MIPS, the first predicted category identified in PENDANT was used.

  • Figure 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 4.

    The activity of GUS in the leaves of two independent transgenic Arabidopsis lines bearing constructs containing the GUS marker gene under the control of the promoter sequence for the P-sensitive gene, SQD1. Plants were grown hydroponically and fully expanded leaves were harvested 20 h before and 4, 28, 100, and 220 h after withdrawing P. Excised leaves were vacuum infiltrated with staining solution containing 520 mg L–1 5-bromo-4-chloro-3-indolyl β-d-glucopyranoside and incubated overnight at 37°C. To assist the visualization of the blue product, chlorophyll was removed from leaves by stepwise replacement of the staining solution with ethanol and mounted in a solution containing 50% (v/v) glycerol. The transgenic lines were GUS13/4 (top) and GUS22/1 (bottom).

Tables

  • Figures
    • View popup
    Table I.

    Genes whose expression was altered 4 h after the withdrawal of P from the nutrient solution

    Elements (P, K, or N) were withdrawn from the nutrient solutions supplied to 28-d-old Arabidopsis plants growing hydroponically. Gene expression profiles were determined in shoots 4 h after the withdrawal of P and 28 h after the withdrawal of K or N. Gene expression was calculated as the ratio of transcript abundance in shoots of plants starved of P, K, or N divided by transcript abundance in shoots of plants supplied with full nutrient solution.

    Gene Expression Relative to Nutrient Replete Plants
    GeneChip IDa Expression Levelb P Starved for 4 h K Starved for 28 h N Starved for 28 h Specificityc Other Stimulid Arabidopsis Genome Initiative (AGI) IDe Functional Categoryf
    1 2 1 2 1 2
    12097_g_at M 0.23 0.03 1.57 1.17 15.26 1.43 -P At2g20870 Expressed protein Unclassified
    14633_at M 0.34 0.14 0.70 3.17 1.03 2.30 -P At5g54190 NADPH:protochlorophyllide oxidoreductase A Control of cellular organisation
    15178_s_at L 0.23 0.18 0.52 0.75 0.71 1.01 -P t, hs, c, a, b At4g14130 Xyloglucan endotransglycosylase (XTR7) Metabolism
    20518_at L 0.39 0.30 1.18 2.11 0.89 3.20 -P At1g10060 LEA76 homolog type 1 Metabolism
    12115_at M 5.84 4.50 3.15 0.63 0.90 0.49 +P ms, c, cc At4g22470 Extensin-like protein Unclassified
    12332_s_at H 18.10 4.27 0.88 0.20 5.30 0.37 +P At3g12500 Basic chitinase Cell rescue, defense, and virulence
    12642_at M 2.54 2.90 1.64 0.71 2.96 0.72 +P At2g15390 Xyloglucan fucosyltransferase, putative Unclassified
    12764_f_at H 2.80 4.20 0.32 1.04 2.38 0.84 +P cc At2g02930 Putative glutathione S-transferase Metabolism
    13154_s_at H 4.48 11.29 2.07 0.13 2.35 0.09 +P cc At2g43590 Putative endochitinase Cell rescue, defense, and virulence
    13244_s_at H 4.91 4.17 3.25 0.47 2.47 0.46 +P w At4g37990 Cinnamyl-alcohol dehydrogenase ELI3-2 Metabolism
    13273_at H 3.17 6.96 2.99 1.11 2.42 0.90 +P hs, ms, cc At4g36990 Heat shock transcription factor HSF4 Transcription
    13467_at H 2.94 2.74 1.08 0.53 1.08 0.76 +P At3g47420 Putative protein Transport facilitation
    13842_at M 4.04 3.71 0.79 0.73 0.75 0.76 +P At1g24140 Putative metalloproteinase Protein fate
    14016_s_at M 6.19 3.38 0.70 0.67 2.58 1.99 +P g, c At1g30700 FAD-linked oxidoreductase family Metabolism
    14032_at M 2.59 3.47 1.78 0.43 3.59 0.58 +P lo, o, s, c At4g37370 Cytochrome P450-like protein Metabolism
    14041_at L 3.45 2.59 0.95 0.79 2.14 0.90 +P At1g09480 Putative cinnamyl alcohol dehydrogenase Metabolism
    14635_s_at M 3.16 7.84 0.83 1.23 2.22 0.72 +P c, d At2g14610 Pathogenesis-related PR-1-like protein Cell rescue, defense, and virulence
    14636_s_at H 6.48 3.96 2.97 3.05 1.96 1.39 +PK w, c, d At1g75040 Thaumatin-like protein Cellular communication
    14638_at H 2.99 2.57 2.13 0.42 2.76 0.35 +P Al, Oz, cc At3g49120 Putative peroxidase Cell rescue, defense, and virulence
    14964_at H 2.91 6.73 1.03 0.45 0.61 0.20 +P At1g65500 Expressed protein Unclassified
    15137_s_at H 2.86 5.70 0.57 0.30 0.89 0.37 +P cc At2g44790 Phytocyanin Unclassified
    15162_at H 9.69 8.20 0.78 0.39 1.85 0.35 +P w, ms At3g04720 Hevein-like protein precursor (PR-4) Unclassified
    15216_at H 2.99 2.89 1.44 1.47 1.38 0.98 +P cc At1g09560 Germin-like protein Metabolism
    15415_at L 4.55 3.29 1.77 0.38 1.68 0.17 +P At1g22900 Disease resistance response protein-related Cell rescue, defense, and virulence
    15665_at M 2.62 5.66 0.20 0.25 2.35 0.50 +P g, c, o At5g04340 Putative c2h2 zinc finger transcription factor Transcription
    15672_s_at H 3.83 4.23 2.33 0.77 0.79 0.47 +P g, cc At2g22470 Arabinogalactan-protein (AGP2) Unclassified
    15866_s_at H 2.99 3.36 1.76 0.95 2.50 0.85 +P At2g38860 Expressed protein Unclassified
    15985_at M 4.03 3.53 0.43 0.61 0.65 0.37 +P Sulf At5g64100 Putative peroxidase Cell rescue, defense, and virulence
    16014_at H 2.89 3.28 0.87 0.43 0.60 0.40 +P g, cc At1g75750 Expressed protein Unclassified
    16053_i_at H 4.10 4.63 2.23 0.51 3.29 0.34 +P g, lo, w At1g02920 Glutathione S-transferase Metabolism
    16150_at H 5.56 9.53 5.84 0.32 11.13 0.19 +P Al, c At4g12480 pEARLI 1 Unclassified
    16198_at M 2.59 3.93 0.63 0.46 1.55 0.36 +P At2g28710 Putative C2H2-type zinc finger protein Transcription
    16888_at M 4.64 4.12 2.24 0.31 2.07 0.30 +P At2g37770 Aldo/keto reductase family Metabolism
    16914_s_at H 19.47 4.44 0.57 0.28 4.14 0.49 +P lo At4g11650 Osmotin precursor Cell rescue, defense, and virulence
    17014_s_at H 3.92 59.55 3.87 0.66 0.57 0.22 +P P, d At2g02990 Ribonuclease, RNS1 Metabolism
    17413_s_at H 14.85 43.39 0.12 0.48 5.73 0.18 +P lo At5g64120 Putative peroxidase Cell rescue, defense, and virulence
    17485_s_at H 44.30 4.66 1.09 0.17 6.02 0.20 +P ms, cc At4g16260 Glycosyl hydrolase family 17 Metabolism
    17533_s_at M 4.62 3.69 5.08 0.19 4.26 0.15 +P t, hs, c, a, b At4g25810 Xyloglucan endotransglycosylase (XTR-6) Metabolism
    17840_at H 2.94 5.31 0.86 0.67 2.41 0.28 +P cc At2g43570 Endochitinase isolog Cell rescue, defense, and virulence
    17894_at H 2.53 5.96 2.28 0.58 1.84 0.40 +P w At2g18690 Expressed protein Unclassified
    17899_at H 4.69 11.87 1.68 0.21 1.35 0.23 +P o At4g15610 Expressed protein Unclassified
    17907_s_at M 5.13 3.55 0.68 0.34 0.32 0.36 +P lo At2g37750 Expressed protein Unclassified
    17930_s_at H 9.13 2.77 0.92 0.41 4.49 0.46 +P ms, lo At4g37520 Peroxidase, prxr2 Cell rescue, defense, and virulence
    17963_at H 2.52 25.79 1.06 0.49 0.79 0.27 +P c At4g12470 pEARLI 1-like protein Unclassified
    18217_g_at H 3.16 6.07 1.30 0.65 2.50 0.68 +P s, c At1g27730 Salt-tolerance zinc finger protein Transcription
    18228_at H 5.83 13.73 3.40 0.65 4.14 0.59 +P ms At3g15356 Lectin-like protein Unclassified
    18591_at M 2.83 3.32 2.16 0.73 2.22 0.38 +P o At5g08790 Expressed protein Unclassified
    18888_at M 3.56 2.55 0.33 0.51 1.12 0.85 +P At1g15380 Expressed protein Unclassified
    18966_at M 2.56 4.93 0.72 0.57 1.25 0.61 +P cc At2g29420 Glutathione transferase, putative Metabolism
    19171_at H 4.46 7.62 2.89 0.34 2.48 0.31 +P ms, cc At2g43510 Putative trypsin inhibitor Unclassified
    19178_at H 3.32 15.50 1.00 0.46 1.07 0.35 +P hl, c, o At5g20230 Blue copper-binding protein Unclassified
    19284_at M 6.02 4.08 1.63 0.77 2.24 0.56 +P ms At2g38240 Putative anthocyanidin synthase Metabolism
    19640_at H 2.54 11.96 3.39 0.54 3.39 0.29 +P ms At2g29460 Putative glutathione S-transferase Metabolism
    19840_s_at M 3.54 6.47 3.72 0.67 1.93 0.29 +P cc At1g30720 FAD-linked oxidoreductase family Metabolism
    19892_at H 2.84 5.76 2.19 0.64 1.40 0.36 +P cc At2g38870 Putative protease inhibitor Protein fate
    19991_at H 2.51 7.87 0.50 0.58 1.77 0.47 +P g At2g35980 Similar to harpin-induced protein hin1 from tobacco Cell rescue, defense, and virulence
    20194_at H 2.94 3.95 6.40 0.53 2.85 0.57 +P lo, cc At2g17500 Expressed protein Unclassified
    20238_at H 3.09 4.09 2.49 1.10 1.95 0.37 +P At3g13790 Glycosyl hydrolase family 32 Metabolism
    20269_at M 4.33 4.13 1.19 0.56 2.34 0.52 +P ms At2g45220 Pectinesterase family Metabolism
    20287_at M 3.74 6.65 2.12 0.66 1.34 0.53 +P w At3g54420 Glycosyl hydrolase family 19 (class IV chitinase) Cell rescue, defense, and virulence
    20420_at M 4.63 3.12 1.52 0.14 1.13 0.11 +P g,c At4g19810 Glycosyl hydrolase family 18/putative chitinase Cell rescue, defense, and virulence
    20491_at H 8.86 4.00 2.85 0.27 2.22 0.28 +P w At2g29350 Putative tropinone reductase Unclassified
    20499_at M 2.96 4.81 2.09 2.60 1.94 2.12 +P At2g33480 Putative NAM (no apical meristem)-like protein Development
    20685_at M 2.55 4.72 2.00 0.85 1.18 0.36 +P o At4g13180 Short-chain alcohol dehydrogenase like protein Metabolism
    • ↵a Affymetrix probe set number. b Qualitative estimates of absolute gene expression, classified as low (L, Affymetrix signal values < 150), medium (M) and high (H, Affymetrix signal values > 800). c Treatments for which genes were differentially expressed 2.5-fold in two biological replicates. (+), Genes whose expression has increased; (-), Genes whose expression has decreased. d Genes whose expression responds to auxin (a); aluminum (Al); brassinosteroids (b); cold (c); cell-cycle regulated (cc); drought (d); gravity (g); high light (hl); heat shock (hs); low oxygen (lo); mechanical stimulus (ms); oxidative stress (o); ozone (Oz); phosphate stress (P); salinity (s); sulfur deficiency (sulf); touch (t); and wounding and/or pathogen attack (w); see text for references. e AGI numbers and brief descriptions of the transcript identified by BLAST searching and from the descriptions provided by Ghassemian et al. (2002). f Functional categories for genes were identified using the AGI number to search the MIPS database (http://mips.gsf.de/proj/thal/db/; 28/11/02), where no category had been experimentally determined the category with the highest probability score was used.

    • View popup
    Table II.

    Genes whose expression was altered 28 and 100 h after the withdrawal of P from the nutrient solution

    Elements (P, K, or N) were withdrawn from the nutrient solutions supplied to 28-d-old Arabidopsis plants growing hydroponically. Gene expression profiles were determined in shoots 28 and 100 h after the withdrawal of P and 28 h after the withdrawal of K or N. Gene expression was calculated as the ratio of transcript abundance in shoots of plants starved of P, K, or N divided by transcript abundance in shoots of plants supplied with full nutrient solution.

    Gene Expression Relative to Nutrient Replete Plants
    GeneChip IDa Time Point Expression Levelb P Starved for 28 h P Starved for 100 h K Starved for 28 h N Starved for 28 h Specificityc Other Stimulid AGI IDe Functional Categoryf
    1 2 1 2 1 2 1 2
    17012_at 28 M 2.53 2.55 0.85 1.12 2.92 1.00 0.95 0.52 +P w, d At1g72260 Thionin Cell rescue, defense, and virulence
    19186_s_at 28 H 3.36 2.91 10.08 2.27 8.81 1.20 1.53 0.47 +P c, w, d, ab, s At3g50970 Dehydrin Xero2 Cell rescue, defense, and virulence
    20641_at 28 H 2.77 3.67 3.31 1.07 2.50 0.47 1.00 0.35 +P d At1g52690 LEA76 homolog type1 Unclassified
    14025_s_at 28/100 M 2.54 3.84 3.05 2.84 2.39 2.49 3.56 2.36 +P At2g04160 Subtilisin-like Ser protease AIR3 Protein fate
    12608_i_at 100 M 0.94 0.60 0.19 0.32 0.92 1.50 0.43 1.05 -P a, b At4g38850 Small auxin up RNA (SAUR-AC1) Unclassified
    13322_at 100 H 0.61 0.68 0.28 0.40 0.42 0.60 0.25 0.54 -P b At4g38860 Putative auxin-regulated protein Unclassified
    13660_i_at 100 L 0.76 0.98 0.27 0.37 1.39 1.66 0.23 0.90 -P a, w At1g15580 IAA5 Transcription
    13972_at 100 M 0.72 0.66 0.36 0.35 0.43 0.71 0.30 0.69 -P At4g17810 SUPERMAN-like protein Transcription
    14048_at 100 M 0.87 0.77 0.28 0.24 0.47 0.81 0.50 1.53 -P c At2g18890 Putative protein kinase Cellular communication
    14946_at 100 H 0.45 0.52 0.36 0.39 0.37 0.22 0.47 0.44 -PK At4g21620 Putative protein Unclassified
    15084_at 100 M 0.75 0.93 0.35 0.25 0.67 0.81 0.31 0.91 -P c At4g35320 Putative protein Unclassified
    15671_s_at 100 M 0.82 1.19 0.40 0.31 0.61 1.11 0.51 1.45 -P w At1g75840 Rac-like GTP binding protein (ARAC5) Cellular communication
    15817_at 100 M 0.53 0.63 0.40 0.34 0.42 0.76 0.33 0.69 -P At4g37240 Putative protein Unclassified
    16312_at 100 M 0.51 0.53 0.39 0.15 0.47 1.10 0.18 1.05 -P At4g12970 Putative protein Unclassified
    18755_at 100 L 1.05 0.79 0.33 0.40 0.68 1.38 1.02 1.90 -P At4g25780 Putative pathogenesis-related protein Cell rescue, defense, and virulence
    20575_at 100 L 0.33 0.92 0.35 0.26 0.32 0.76 0.37 1.52 -P At4g32890 Putative protein Transcription
    12341_s_at 100 M 1.00 1.53 2.61 4.42 1.76 0.71 3.08 0.76 +P ms At4g20110 Vacuolar sorting receptor-like protein Protein fate
    12500_s_at 100 M 2.86 1.56 5.06 4.87 5.62 1.00 5.48 0.65 +P d At1g51760 Indole acetic acid-Ala hydrolase (IAR3) Unclassified
    12597_at 100 M 0.83 0.61 5.36 2.63 0.58 1.46 2.17 1.28 +P At2g22780 Putative glyoxysomal malate dehydrogenase precursor Energy
    12880_at 100 H 2.18 1.33 2.80 5.33 2.02 1.05 2.96 0.63 +P w, d, g At3g28930 AIG2-like protein Unclassified
    13004_at 100 M 1.39 2.16 6.39 3.20 4.12 9.54 2.90 4.71 +PKN c, s At2g17840 Putative senescence-associated protein 12 Unclassified
    13230_at 100 H 2.00 0.76 2.89 3.11 0.03 0.95 3.81 1.14 +P At4g16190 Cys proteinase Energy
    13666_s_at 100 M 2.10 1.03 2.85 2.88 5.28 1.04 4.35 1.02 +P At2g04400 Putative Indole-3-glycerol phosphate synthase Metabolism
    13695_at 100 M 1.37 0.94 3.72 2.76 0.83 1.34 1.70 1.87 +P w At3g20600 Non-race-specific disease resistance protein (NDR1) Cell rescue, defense, and virulence
    13934_g_at 100 M 2.58 1.81 2.53 3.43 3.03 2.38 6.32 1.71 +P At4g17230 Scarecrow-like 13 (SCL 13) Transcription
    14016_s_at 100 M 2.33 1.37 2.80 2.54 0.70 0.67 2.58 1.99 +P g, c At1g30700 FAD-linked oxidoreductase family Metabolism
    14032_at 100 M 1.83 1.37 6.30 5.18 1.78 0.43 3.59 0.58 +P o, c, lo, s At4g37370 Cytochrome P450-like protein Metabolism
    14116_at 100 H 2.52 1.17 6.06 2.55 1.88 1.00 4.72 0.92 +P cc At5g26340 Hexose transporter-like protein Transport facilitation
    14614_at 100 M 1.83 1.49 3.62 3.41 1.40 1.22 2.14 0.80 +P cc At2g30140 Putative glucosyltransferase Metabolism
    14672_at 100 H 2.38 1.30 5.56 2.80 0.98 1.50 3.88 1.44 +P cc, d, g At3g54640 Tryptophan synthase α-chain Metabolism
    14978_at 100 M 2.66 2.07 2.69 6.34 1.00 0.94 3.56 1.27 +P At2g43820 Putative glucosyltransferase Metabolism
    15124_at 100 H 2.61 1.24 2.60 8.41 1.96 0.79 2.75 0.36 +P g, c At3g30775 Osmotic stress-induced Pro dehydrogenase Metabolism
    15156_at 100 H 1.68 1.10 3.14 5.18 1.01 2.05 3.69 1.84 +P At5g50850 Pyruvate dehydrogenase E1 component β-subunit Metabolism
    15195_s_at 100 H 2.82 1.29 3.87 2.86 4.52 0.82 3.09 0.64 +P cc At2g30490 Cinnamate-4-hydroxylase Metabolism
    15616_s_at 100 H 1.06 2.24 2.85 7.28 2.69 4.35 5.65 2.11 +PK At1g21250 Ser-Thr kinase Cellular communication
    15629_s_at 100 H 2.52 1.93 5.08 3.85 4.70 1.07 4.88 0.66 +P At1g17740 Phosphoglycerate dehydrogenase Energy
    15656_at 100 M 1.00 0.76 2.72 3.61 1.41 0.68 1.93 1.15 +P At5g54080 Homogentisate 1,2-dioxygenase Unclassified
    15866_s_at 100 H 1.20 1.03 2.79 2.47 1.76 0.95 2.50 0.85 +P At2g38860 Expressed protein Unclassified
    15976_at 100 M 0.68 1.10 3.09 5.52 1.44 2.21 2.15 1.05 +P cc, sulf At1g21750 Putative protein disulfide isomerase precursor Protein fate
    16053_i_at 100 H 1.84 0.94 4.71 3.70 2.23 0.51 3.29 0.34 +P g, lo, w At1g02920 Glutathione S-transferase Metabolism
    16077_s_at 100 M 1.22 1.33 3.36 3.04 1.39 2.73 3.87 1.64 +P hm At5g44070 Phytochelatin synthase Unclassified
    16440_at 100 M 1.33 1.08 2.53 4.46 2.20 1.02 2.14 0.47 +P lo, c, o At2g40000 Putative nemalode-resistance protein Cell rescue, defense, and virulence
    16493_at 100 H 2.35 1.89 2.59 3.71 8.84 0.63 2.53 0.71 +P s, c At1g54010 Myrosinase-associated protein Metabolism
    16609_at 100 M 1.74 0.72 4.12 2.64 1.32 0.76 5.50 1.09 +P w, e, cc At5g47220 Ethylene-responsive element-binding factor 2 (EREB2) Transcription
    17104_s_at 100 H 1.86 1.36 2.72 2.98 4.47 0.62 3.62 0.38 +P At4g35630 Phospho-Ser aminotransferase Metabolism
    17105_at 100 M 2.94 1.07 2.95 3.44 3.28 1.10 7.11 1.32 +P w, lo At5g47910 Respiratory burst oxidase protein Cell rescue, defense, and virulence
    17207_at 100 M 1.83 0.82 2.70 3.82 1.43 0.67 4.05 0.72 +P At4g36670 Sugar transporter like protein Metabolism
    17413_s_at 100 H 6.29 0.36 8.64 5.51 0.12 0.48 5.73 0.18 +P lo At5g64120 Putative peroxidase Cell rescue, defense, and virulence
    17484_at 100 M 0.52 2.95 3.37 3.17 1.30 0.70 0.54 0.45 +P At1g17020 SRG1-like protein Metabolism
    17775_at 100 M 1.42 0.84 4.14 2.70 0.77 0.48 3.08 0.47 +P w, ms At1g61800 Glc-6-phosphate/phosphate-translocator precursor Transport facilitation
    17877_g_at 100 H 1.54 1.73 2.77 2.66 2.36 0.71 1.92 0.49 +P lo At4g15760 Monooxygenase Metabolism
    17917_s_at 100 H 1.07 1.53 4.56 3.68 1.73 2.54 2.49 1.94 +P At2g41090 Putative calcium binding protein CaBP-22 Cellular communication
    17930_s_at 100 H 3.07 1.68 7.35 3.27 0.92 0.41 4.49 0.46 +P ms, lo At4g37520 Peroxidase, prxr2 Cell rescue, defense, and virulence
    18228_at 100 H 2.29 0.96 5.23 3.21 3.40 0.65 4.14 0.59 +P ms At3g15356 Lectin-like protein Unclassified
    18946_at 100 M 3.05 0.48 3.46 2.88 5.39 0.31 4.19 0.29 +P ms At5g39580 Peroxidase ATP24a Cell rescue, defense, and virulence
    19373_at 100 M 0.77 1.67 2.71 3.46 0.80 1.09 2.55 2.16 +P At2g29670 Expressed protein Unclassified
    19614_at 100 H 2.78 2.05 3.28 3.77 3.62 0.15 0.68 0.23 +P At1g09500 Putative cinnamyl alcohol dehydrogenase Metabolism
    19640_at 100 H 2.97 1.60 4.31 3.81 3.39 0.54 3.39 0.29 +P ms At2g29460 Putative glutathione S-transferase Metabolism
    19704_i_at 100 H 4.82 1.23 3.98 4.42 1.77 1.09 4.94 1.49 +P ms At5g24160 Squalene monooxygenase 1,2 (squalene epoxidase 1,2) Metabolism
    19843_at 100 M 2.84 0.92 3.11 3.19 2.16 1.16 3.69 2.14 +P At1g61890 Expressed protein Transport facilitation
    19844_at 100 M 1.13 0.69 2.57 3.60 1.79 0.72 2.52 0.63 +P w At4g38540 Monooxygenase 2 (MO2) Metabolism
    19991_at 100 H 1.00 0.95 6.61 2.66 0.50 0.58 1.77 0.47 +P g At2g35980 Similar to harpin-induced protein hin1 from tobacco Cell rescue, defense, and virulence
    20344_at 100 M 0.93 1.72 2.88 2.79 1.20 2.02 1.02 1.74 +P At2g15090 Putative fatty acid elongase Metabolism
    20442_i_at 100 H 0.97 0.75 2.63 2.87 1.49 0.32 1.52 0.74 +P At1g16410 Putative cytochrome P450 protein Metabolism
    • ↵a Affymetrix probe set number. b Qualitative estimates of absolute gene expression, classified as low (L, Affymetrix signal values < 150), medium (M), and high (H, Affymetrix signal values > 800). c Treatments for which genes were differentially expressed 2.5-fold in two biological replicates. (+), Genes whose expression has increased; (-), Genes whose expression has decreased. d Genes whose expression responds to auxin (a); abscisic acid (ab); brassinosteroids (b); cold (c); cell-cycle regulated (cc); drought (d); ethylene (e); gravity (g); high light (hl); heat shock (hs); low oxygen (lo); mechanical stimuli (ms); salinity (s); sulfur deficiency (sulf); and wounding and/or pathogen attack (w); see text for references. e AGI numbers and brief descriptions of the transcript identified by BLAST searching and from the descriptions provided by Ghassemian et al. (2002). f Functional categories for genes were identified using the AGI number to search the MIPS database (http://mips.gsf.de/proj/thal/db/; 28/11/02), where no category had been experimentally determined the category with the highest probability score was used.

    • View popup
    Table III.

    Genes selected for quantitative PCR to confirm Affymetrix GeneChip results

    Genes were selected to have contrasting magnitudes (low, L; medium, M; or high, H) and change in gene expression when assayed using Affymetrix GeneChips in response to the withdrawal of P from hydroponcally grown 28-d-old Arabidopsis for 4, 28, and 100 h. The primers used for quantitative PCR are indicated. -, not determined.

    Expression Level GeneChip Analysis GeneChip ID AGI ID Forward Primer Reverse Primer Mean-Fold Change on GeneChip Fold Change for Quantitative PCR
    P Starved for 4 h P Starved for 28 h P Starved for 100 h P Starved for 4 h P Starved for 28 h P Starved for 100 h
    L Down at 4 h 20518_at At1g10060 AATAGAGGGGATGAAAGC ATGAACAGAAGGAGAATGC 0.34 1.23 0.44 1.00 0.78 0.20
    H Up at 4 h 17963_at AT4g12470 CCTCTCTTGCTCTTTTCTTTG GGGACTGGCTTTGGTTTAG 14.15 1.43 0.96 0.14 1.78 0.01
    H Up at 4 + 28 h 17014_s_at At2g02990 CTTGCCTTCTGTCTTCTCTG GGATAACAACACTTCTTCTGTG 31.73 4.77 1.88 3.33 11.41 8.45
    M Down at 100 h 14048_at At2g18890 GGATAACAAGAGGAGGAAGAGATG CAACAACCAAGAAGAGACAAGAC 0.58 0.82 0.26 0.97 1.50 0.42
    M Up at 100 h 12597_at At2g22780 GCTTCCCTTCTTCGCATC GCCTTCTCTAATCCCATCCTC 1.57 0.72 4.00 1.52 1.79 1.54
    H Up at 100 h 14116_at At5g26340 GCCGTTCCGTTGTTCTTG CTTGGCGGTCCCATAGTTG 2.35 1.85 4.31 0.32 4.45 0.77
    H Up at 100 h 15629_s_at At1g17740 GAAGGGGAGGTTGAAAGTGG CACCGTATTAGCCGTTGGAG 3.74 2.22 4.47 0.29 4.79 3.23
    H Up at 100 h 17104_s_at At4g35630 ACACGCCTCCTTGCTTTG GCTTTCCTCTGGTTCTTCTTCTC 2.01 1.61 2.85 0.60 5.45 3.08
    M Up at 100 h 17775_at At1g61800 AAGAAAGGGATGAAAGGGAAG CACGGCAATAGAAAATGGAG 2.74 1.13 3.42 1.11 19.76 5.14
    - - Not present 18s rRNA CATAAACGATGCCGACCAG AGCCTTGCGACCATACTCC 1.13 1.25 1.15
    - - Not Present IPS1 AGGGGATGGCCTAAATACAAAATG GGGAGATAAACAAAACTCGCAGTC 0.89 14.68 1143.05
    - - Not Present SQD1 CACCACCCGAAACATCTACC ACCGCAATAACCATCTCCAC 0.68 2.1 4.5
    • View popup
    Table IV.

    The occurrence of novel cis-regulatory elements in the promoters of genes whose expression changed early or late in response to P withdrawal in the experiments reported here (Tables I and II) and cis-regulatory elements previously identified as common to genes whose expression responded to P starvation

    The occurrence of these cis regulatory elements in the promoters of all genes on the Affymetrix GeneChip are given for comparison. —, not determined.

    No. of Genes with Element Upstream of Start Codon
    Element Name Element Sequence Early P-Responsive Genes Late P-Responsive Genes Affymetrix GeneChip Reference
    No. % No. % No. %
    Novel elements
        PHO-like C(G/T/A)(C/T/A)GTGG 18 32.1 — — 588 7.1 —
        TATA box-like TATAAATA 20 35.7 — — 753 9.1 —
    P-responsive elements
        PHR1-binding site GNATATNC 10 16.7 9 17.6 1498 18.2 Rubio et al. (2001)
        PHO element CACGT(G/C) 17 28.3 16 31.4 1574 19.1 Mukatira et al. (2001)
    ATGCCAT 1 1.7 2 3.9 349 4.2 Mukatira et al. (2001)
        Helix-loop-helix CA(T/G)(A/C)TG 32 53.3 23 45.1 4431 53.7 Mukatira et al. (2001)
        NIT 2 TATC(A/T)(A/T) 42 70.0 36 70.6 6296 76.3 Mukatira et al. (2001)
PreviousNext
Back to top

Table of Contents

Print
Download PDF
Email Article

Thank you for your interest in spreading the word on Plant Physiology.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants
(Your Name) has sent you a message from Plant Physiology
(Your Name) thought you would like to see the Plant Physiology web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants
John P. Hammond, Malcolm J. Bennett, Helen C. Bowen, Martin R. Broadley, Dan C. Eastwood, Sean T. May, Clive Rahn, Ranjan Swarup, Kathryn E. Woolaway, Philip J. White
Plant Physiology Jun 2003, 132 (2) 578-596; DOI: 10.1104/pp.103.020941

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants
John P. Hammond, Malcolm J. Bennett, Helen C. Bowen, Martin R. Broadley, Dan C. Eastwood, Sean T. May, Clive Rahn, Ranjan Swarup, Kathryn E. Woolaway, Philip J. White
Plant Physiology Jun 2003, 132 (2) 578-596; DOI: 10.1104/pp.103.020941
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
    • Abstract
    • RESULTS
    • DISCUSSION
    • MATERIALS AND METHODS
    • Acknowledgments
    • Footnotes
    • LITERATURE CITED
  • Figures & Data
  • Info & Metrics
  • PDF

In this issue

Plant Physiology: 132 (2)
Plant Physiology
Vol. 132, Issue 2
Jun 2003
  • Table of Contents
  • About the Cover
  • Index by author
View this article with LENS

More in this TOC Section

  • Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping
  • Characterization of the Early Response of Arabidopsis to Alternaria brassicicola Infection Using Expression Profiling
  • Rapid, Noninvasive Screening for Perturbations of Metabolism and Plant Growth Using Chlorophyll Fluorescence Imaging
Show more RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Similar Articles

Our Content

  • Home
  • Current Issue
  • Plant Physiology Preview
  • Archive
  • Focus Collections
  • Classic Collections
  • The Plant Cell
  • Plant Direct
  • Plantae
  • ASPB

For Authors

  • Instructions
  • Submit a Manuscript
  • Editorial Board and Staff
  • Policies
  • Recognizing our Authors

For Reviewers

  • Instructions
  • Journal Miles
  • Policies

Other Services

  • Permissions
  • Librarian resources
  • Advertise in our journals
  • Alerts
  • RSS Feeds

Copyright © 2021 by The American Society of Plant Biologists

Powered by HighWire