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. 2003 Dec;15(12):3033–3050. doi: 10.1105/tpc.017574

Table 2.

Genes That Are Expressed Differentially in Pti4-Expressing Plants Compared with Wild-Type Plants

SAGE Tag Identifier a Tag Sequence b Tag Count c
Fold d GenBank
Accession
Number		 Corresponding Gene e Promoter f
Wild
Type		 Pti4
Environmental/pathogen response (PR and antimicrobial genes, and drought- and salt-responsive genes) g
65 CATATTTCTG 0 34 33.1 T04323 Antifungal protein PDF1.2 P
174 TGTCAAGGAG 3 11 3.6 U40399 Cytosolic cyclophilin ROC3
212 TCGTGTTTGG 2 10 4.9 U42724 Chloroplast stromal cyclophilin ROC4 P
243 GAGGAACTAA 1 10 9.7 X78584 Drought-induced Di19 P
356 GTAGTGACCA 1 7 6.8 X98189 Peroxidase ATP1a P
523 GTGCATTTGG 1 5 4.9 AF003728 Salt-induced plasma membrane intrinsic
  protein SIMIP h 		P
642 ATGGAATGCT 0 5 4.9 AA395048 Thylakoid lumen rotamase (cyclophilin) P
643 GATTATAATG 0 5 4.9 D89051 Drought-induced putative sugar transporter ERD6
854 CTTGTTTCGG 0 4 3.9 U01880 Hevein-like protein precursor (PR-4) h P
617 ACCGGACACA 5 1 −5.1 AV527586 Putative protein, disease resistance
  protein family (LRR) h 		P
634 CAACTCCTCA 6 0 −6.2 BE038927 Major latex protein (MLP)-related P
Signal transduction (transcription factors, kinases, signaling molecules)
352 GGACGTGCCG 0 8 7.8 X91259 Similar to putative lectin P
423 AAGAAGTTTT 1 6 5.8 U27698 Putative calreticulin AtCRTLh P
427 GACAACCTGA 1 6 5.8 AJ242970 General transcription factor BTF3b homologh P
844 AATCGCGTCA 0 4 3.9 AA598125 Receptor-protein kinase-like proteinh P
274 GCACAAACAA 9 2 −4.6 At5g02030 i Homeodomain protein
347 AGTTGTTTTT 7 2 −3.6 AB013886 Transcription factor RAV1h P
503 ACTCTTTTAA 6 1 −6.2 AF285106 CBL-interacting protein kinase CIPK6 h P
832 CGAGGAAGCA 5 0 −5.1 Y12710 Shaggy-related protein kinase, ASK-GAMMA
Cell cycle, growth, and proliferation
104 AAGATTAAGG 5 16 3.1 U41998 Actin2
646 GGAAAGAACT 0 5 4.9 AY058193 Expansin At-EXP6
Detoxification
639 AAGAACGGAC 0 5 4.9 Z25705 Putative cytochrome P450
842 AAAACTCGGT 0 4 3.9 U37697 Glutathione reductase h P
636 TCTTATGTCA 6 0 −6.2 AV556265 Putative M-type thioredoxin P
Fatty acid, phospholipid, and isoprenoid metabolism
645 GCTGCAAACC 0 5 4.9 AB007799 NADH-cytochrome b5 reductase P
208 CAGGTTGTGG 10 3 −3.4 AV547952 Putative acetyl-CoA synthetase
620 GAGGCCAAGG 5 1 −5.1 AJ010713 β-Ketoacyl-CoA synthase family (FIDDLEHEAD) h
631 TTTAAGATAT 5 1 −5.1 AF159801 Lipid transfer protein ltp4h
Energy metabolism and photosynthesis
189 GATTGAAGTT 2 11 5.4 BT002151 Putative Thr synthase
321 GGTGAAATTT 1 8 7.8 L44582 Vacuolar H+-pumping ATPase ava-p2 P
422 AAATTGATCT 1 6 5.8 X97484 Putative phosphate transporter h P
637 AACAACAAAA 0 5 4.9 AV547395 Amino acid permease AAP2
640 AGCGTTCTCC 0 5 4.9 Z29881 Putative fructose 1,6-bisphosphatase P
4 AAGGTGTGGC 200 146 −1.4 BE039376 Rubiscoj small subunit 2b precursor
8 CTTGTGATGG 155 111 −1.4 X14212 Rubisco activase
17 TTTGTACAAA 57 37 −1.6 AF134120 Chlorophyll a/b binding protein Lhca2
20 TTCTCTATGT 55 32 −1.8 AF134124 Chlorophyll a/b binding protein Lhcb2
27 AAAGCTTTCT 46 25 −1.9 AJ245629 Putative photosystem I subunit III precursor
31 TTTCTATAAA 40 23 −1.8 X55970 Photosystem II 10-kD polypeptide
91 ATCATTCGTG 18 7 −2.6 AA586203 Transketolase-like protein
110 TTACCTTTCT 15 6 −2.6 AJ245631 Photosystem I subunit VI precursor
112 TACTTACATT 17 4 −4.4 AV559242 Putative glycolate oxidase
318 TTTATTTTTC 9 1 −9.2 S74719 Sedoheptulose-1,7-bisphosphatase P
508 TTTGTATTCT 6 1 −6.2 AV557139 H+-transporting ATPase-like protein h
834 CTTTGTGATG 5 0 −5.1 AA598190 Similar to Rubisco activase P
836 GCTATACAAA 5 0 −5.1 AI993835 Vacuolar H+-transporting ATPase chain E
838 GTACAGCGCC 5 0 −5.1 N96033 Putative dihydroxyacetone kinase
Ribosomal proteins
355 CTGGGAAAAA 1 7 6.8 AV549039 50S ribosomal protein L27 P
357 TCCTTCAAGA 1 7 6.8 BE038325 Ribosomal protein S13-like P
419 AAGAGCCGAG 0 7 6.8 Y09635 50S ribosomal protein L24, chloroplast precursor P
647 GTTCGTTGAG 0 5 4.9 AY063876 Putative plastid ribosomal protein L34 precursor
209 GTGAGACTTG 10 3 −3.4 AV554596 40S ribosomal protein-like
275 GACGTATTGA 10 1 −10.3 AI100025 Putative ribosomal protein L18 P
317 GGACCACCAC 9 1 −9.2 AA728511 60S ribosomal protein L10A P
351 TGTACTTTGT 8 1 −8.2 AI100051 Ribosomal protein S1
506 GTTTTATATA 6 1 −6.2 T43594 60S ribosomal protein L38-like protein h P
511 TGTCTTAGCT 7 0 −7.2 AA597822 Putative 60S ribosomal protein L21 P
833 CTTCCGTGTT 5 0 −5.1 L28828 Ribosomal protein S11
Protein processing/fate
635 CTTTTTAAGG 6 0 −6.2 AA712419 ATP-dependent Clp protease ATP
  binding subunit (ClpC1)		 P
Membrane proteins
125 GTTTCGCCGA 14 5 −2.9 AF097648 Phosphate/triose phosphate translocator precursor
210 TGAATTTGTA 11 2 −5.6 Y08061 Endomembrane-associated protein P
242 TGTGATGATC 10 2 −5.1 AA728495 Water channel–like protein P
Other categories
30 TGTAGCTCAG 0 63 60.8 AF187951 Octopine synthase 3′ terminator region from
  Pti4 and nptII gene cassettes
244 ATGGTGATTA 2 9 4.4 AF195896 Arabinogalactan protein AGP15
512 AAGCAACTCT 0 6 5.9 AF017074 RNA polymerase I, II, and III 16.5-kD subunit P
509 CAAAAAAAAA 7 0 −7.2 AY042804 Putative RNA binding protein
837 GCTCCGCTCC 5 0 −5.1 AV566796 Putative glycine dehydrogenase
841 TTTCGTCTTG 5 0 −5.1 AV557387 Putative xyloglucan endotransglycosylase
Unknown proteins
173 CATTTGGATT 3 11 3.6 AV536971 Unknown protein
211 AGAATGGTTG 2 10 4.9 AI099719 Unknown protein
425 CCTTGATGTT 1 6 5.8 R90105 Unknown protein h P
648 TGAAAGTTGT 0 5 4.9 AY045836 Unknown protein
19 ATAGAACCTT 52 35 −1.5 BE038487 Unknown protein
70 AATTGGAATG 23 11 −2.2 AY065156 Unknown protein
171 AGAAGAAGCC 15 0 −15.4 At5g40700 i Unknown protein
418 CAATTAGAGT 7 1 −7.2 AV534110 Unknown protein
829 AAGGAGTTGT 5 0 −5.1 AY070394 Unknown protein
830 ACAAAATTTT 5 0 −5.1 AY035176 Unknown protein
a

SAGE tag identifier corresponding to a particular gene.

b

The 10-bp SAGE tag sequence, excluding the 5′ adjacent NlaIII site (CATG).

c

Number of tags retrieved from the wild-type and Pti4 libraries.

d

Fold increase or fold decrease of tag numbers observed in Pti4 plants compared with wild-type plants. Genes with decreased tag numbers in Pti4-expressing plants are designated with a minus sign.

e

The gene corresponding to the tag. For each functional category, the genes with increased tag numbers in Pti4-expressing plants are shown first, followed by the genes with decreased tag numbers in Pti4-expressing plants. Within these categories, tags are shown in order of SAGE tag identifiers.

f

P indicates that the promoter of the gene was analyzed (see Table 3).

g

The genes are grouped into different functional categories.

h

The difference in tag number between the wild-type and Pti4 libraries for these genes was significant at 0.05 ≤ P ≤ 0.15. For all other genes, the difference in tag number was significant at P ≤ 0.05.

i

The TAIR locus name. GenBank or EST clones containing the SAGE tag could not be identified for these genes.

j

Rubisco, ribulose-1,5-bisphosphate carboxylase/oxygenase.