Table II.

A complete list of sequenced genes up-regulated by nitrate

Clone IDAccession No.GenBank HitGene/cDNA CloneExpression (h after treatment)1-h/24-h Signal Ratios
B6-1 AW979398 D30719 Dehydration-induced protein (ERD15)Down after 6 h1.5/0.7
E5-1 AW979904 L42814 Acetyl coenzyme A carboxylaseUp 6–12 h0.9/1.4
F4-1 AW979983 Z46944 Non-photosynthetic ferredoxinUp 1–96 h1.6/1.4
H5-1 AW219021 Z97335 HydroxymethyltransferaseUp 1–96 h2/1.8
H8-1 AW219174 X79770 sti (stress-inducible protein)Up 6–96 h1/2.4
J3-1 AW219553 U55838 Carbonic anhydraseUp 1–12 h1.7/1
J4-1 AW219399 O24661 Asp synthetaseUp 1–96 h2.8/2
J12-1 AW219540 A44133 Phe ammonia-lyaseDown after 6 h1.2/0.7
I13-1 AW219330 JA0177Salt-induced proteinUp after 1 h2/1
D6-1 AW224693 AB004307 Ferredoxin-NADP oxidoreductaseUp 1–12 h2/2.4
I4-4 AW624841 X92975 Xyloglucan endo-transglycosylaseUp 6–96 h1.6/1.8
K6-4 AW625018 P08440 Fru-bisphosphate aldolaseUp 1–6 h2/0.8
L1-4 AW218551 AF104925 2-Oxoglutarate-dependent dioxygenaseUp 1–96 h1.4/1.6
M5-4 AW625127 AF183891 S-Adenosyl-l-methionine synthetase (sam2)Up 1–96 h1.2/2
A19-4 AW624860 AF022775 Caffeoyl-coenzyme A 3-O-methyltransferaseDown after 6 h1.7/0.9
B7-4 AW154870 AF007581 Cytoplasmic malate dehydrogenaseUp 1–6 h2.2/1.1
B18-4 AW979983 Z46944 Non-photosynthetic ferredoxinUp 1–12 h1.3/1
B22-4 AW219992 U64924 NTGP3 (small GTP-binding protein)Down after 6 h0.7/1
E4-4 AW218294 AF092547 ProfilinUp 6–48 h1.1/1.7
E9-4 Y18931 Y18931 Tomato subtilisin-like proteaseUp after 6 h1/1.8
E16-4 AW224694 O04397 Ferredoxin-NADP reductaseUp 1–6 h1.4/0.9
F20-1 AW218899 D88156 Tropinone reductase-IDown after 12 h1.6/0.8
D18-2 BG713773 S20925 PolyubiquitinDown 6–12 h1.3/1.1
H5-2 BG713782 X99100 Protein kinaseUp 6–12 h1/1.4
F5-2 BG713776 Z48976 Phosphoglycerate kinaseUp 6–96 h0.9/2
G4-2 BG713778 AF112440 Ribosomal protein S26Up 1–48 h1.5/1.8
H12-2 BG713785 U17005 Glyceraldehyde-3-phosphate dehydrogenaseUp 1–48 h0.8/1.6
H23-2 BG713787 T04367 Water channelDown 6–48 h1.4/0.6
J8-2 BG713790 U90212 DNA-binding protein ACBFUp 12 h1/1.4
J9-2 BG713791 AC016662 EnolaseUp 1–96 h2.2/3
J10-2 BG713792 AC016662 EnolaseUp 48 h1.1/1.4
J11-2 BG713793 AC016662 EnolaseUp 6–48 h1/1.8
K13-2 BG713798 AB001891 Ribosomal proteinUp 6–48 h0.8/2
L5-2 BG713800 X98063 PolyubiquitinUp 6–48 h1.2/1.5
M7-2 BG713803 T06434 Water channelDown 6–12 h1/1.3
N5-2 BG713805 A48767 Glu decarboxylaseUp 1–48 h1.7/1
N6-2 BG713806 L44142 Auxin-repressed proteinUp 1–48 h1.4/1.8
A10-3 BG713808 T02215 Ferrodoxin reductaseUp 1–6 h1.5/1
C23-3 BG713812 T01984 LEA 5 proteinDown 6–48 h4.2/1.3
D2-3 BG713813 S51584 PeroxidaseUp 12 h1.1/1.8
E4-3 BG713815 T03673 EnolaseUp 1–96 h1/1.7
G3-3 BG713818 U44386 LEA 5 proteinUp 1–12 h2/1.5
H3-3 BG713822 AL163816 Glutaredoxin-like proteinUp 6 h1.8/0.9
H5-3 BG713824 Y10024 Ubiquitin extension proteinUp 12–48 h1.1/1.6
J10-3 BG713829 Y15371 Induced by nod factorUp 48 h0.9/1.4
L13-3 BG713835 M94135 Chloroplast carbonic anhydraseUp 1 h1.8/1

This table includes nitrate-induced genes that were not subjected to northern analysis. For 18 of the sequenced nitrate-induced clones, we did not find sequence homology with any known genes in GenBank and thus these were not included in the Table. Genes with a clone ID ending in “−1” were identified from the Cornell tomato root cDNA libraries that were generated in collaboration with Dr. Steve Tanksley and sequenced by the Institute for Genomic Research. All other clones were obtained from the subtractive DNA libraries. The column labeled “1-h/24-h Signal Ratios” shows the quantified change in gene expression for plants exposed to nitrate for either 1 or 24 h compared with control plants (N withheld for 48 h).