Table 4.

Number of Clones Involved in Different Functional Groups Upregulated or Downregulated at Least Two-Fold by White Light

PathwaysGene
 NumberRepresentative Gene Namesa
Upregulated
 Photosynthetic light
 reactions5617 CAB genes, 15 PSI proteins, 14 PSII proteins, 10 proteins involved in electron transport and ATP synthesis
 Photosynthetic carbon
 metabolism254 RBCS genes, 2 phosphoglyceate kinases, 2 GAPDHs, triose-phosphate isomerase, aldolase, fructose-1,6-phosphate phosphatase, 3 fructose-1,6-bisphosphate aldolases, transketolase, sedoheptulose 1,7-bisphosphate phosphatase, ribulose-5-phosphate epimerase, 2 ribose-5-phosphate isomerases, ribulose-5-phosphate kinase, ferredoxin, 2 thioredoxins, 2 ferredoxin-thioredoxin reductases, Rubisco activase
 Starch synthesis3Fructose-1,6-bisphosphate aldolase, fructose-1,6-bisphosphate phosphatase, pyrophosphorylase
 Sucrose synthesis5Phosphate/triose phosphate translocator, cytosolic triose-phosphate isomerase, cytosolic fructose-1,6-bisphosphate aldolase, phosphofructokinase, sucrose synthase
 Photorespiration84 RBCS genes, glycolate oxidase, catalase, hydroxypyruvate reductase, glycine decarboxylase
 Glycolysis5Fructokinase, triose phosphate isomerase, pyruvate kinase, pyruvate decarboxylase, alcohol dehydrogenase
 Trichloroacetic acid cycle5Pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, phosphopyruvate hydratase, malate dehydrogenase
 Cell wall synthesis and
 cell wall protein8Cellulose synthase, glucosyltransferase, β-1,2-xylosyltransferase, UDP-glucose:glycoprotein glucosyltransferase, cell wall–plasma membrane linker protein, proline-rich protein, extensin, AGP
 Protein synthesis in
 chloroplast5611 50S ribosomal proteins, 4 30S ribosomal proteins, 7 other ribosomal proteins, 9 initiation and elongation factors, 9 aminoacyl-tRNA synthetases, 6 RNA helicases, 10 chaperonines
 Protein synthesis in
 cytoplasm6015 60S ribosomal proteins, 3 40S ribosomal proteins, 8 other ribosomal proteins, 9 initiation and elongation factors, 9 aminoacyl-tRNA synthetases, 6 RNA helicases, 10 chaperonins
 Phenylpropanoid
 biosynthesis8PAL1, CHS, caffeoyl-CoA O-methyltransferase, cinnamyl-alcohol dehydrogenase, O-methyltransferase, GST, glutathione-conjugate transporters, cytochrome P450
 Amino acid synthesis
 pathways15Dehydrogenase, glutathione peroxidase, Δ-1-pyrroline-5-carboxylate synthetase, phosphoribosylglycinamide synthetase, histidinol dehydrogenase, acetolactate synthase, aminotransferase, adenine phosphoribosylanthranilate transferase, phosphoribosylanthranilate transferase, uridylyl transferase, glutamine synthetase, glutamate/ornithine acetyltransferase, 3-isopropylmalate dehydratase, glutathione reductase, tryptophan synthase
 Chlorophyll and heme
 synthesis4Ferrochelatase, glutamyl-tRNA reductase, protoporphyrinogen IX oxidase, glutamate-1-semialdehyde 2,1-aminomutase 1
 Transcription factors15G-box binding factor, B-box zinc finger, 2 bHLH transcription factors, 3 MYB-related transcription factors, SCARECROW-like factor, zinc finger transcription factor–like protein, AP2 domain transcription factor-like protein, bZIP transcription factor, transcription factor HUA2, transcription factor II homolog, homeobox leucine zipper protein, putative transcription factor
 Uniquitin-proteasome
 pathway234 polyuniquitin and ubiquitin genes, 9 26S proteasome subunits, 2 proteasome subunit–related proteins, E1, E2, and 6 E3 genes
Downregulated
 Ethylene biosynthesis3ACC synthase, ACC oxidase, SAM synthase
 BR biosynthesis424-sterol C-methyltransferase, C-8,7-sterol isomerase, 3-β-hydroxysteroid dehydrogenases, steroid sulfotransferase
 Cell wall degradation and
 cell wall proteins26Cellulase, XET, 2 expansins, xylosidase, xyloglucan endo-1,4-β-d-glucanase, endo-1,4-β-d-glucanase, 1,3-β-glucanase, xylose isomerase, pectinesterase, pectate lyase, 7 peroxidases, 2 extensin homologs, glycine-rich protein, AGP4, 2 proline-rich cell wall proteins, hydroxyproline-rich protein, pollen surface protein homolog
 Water transport across
 tonoplast55 aquaporins in tonoplast
 Water transport across
 plasma membrane55 water channel and membrane intrinsic proteins in plasma membrane
 Sulfur assimilation92 GSTs, sulfate adenylyltransferase, sulfate transporter, phytochelatin synthase, cysteine synthase, cytochrome P450 monooxygenase, 2 ABC transporters
 Nitrogen assimilation93 nitrate transporters, 2 AS proteins, glutamine synthetase, glutamate dehydrogenase, serine carboxypeptidase, cysteine synthase
 Fatty acid oxidation5Glycerol-3-phosphate dehydrogenase, inorganic pyrophosphatase, ketoacyl-CoA thiolase, malic enzyme, acyl-CoA oxidase
 Glyoxylate cycle4isocitrate lyase, citrate synthase, malate synthase, malate dehydrogenase
 Transcription factors183 AP2 domain transcription factors, 2 MYB-related transcription factors, transcription factor L2, transcription factor tga1, transcription factor EREBP, MADS box transcription factor–like protein, TATA box binding protein, transcription factor–like protein, putative HLH DNA binding protein, homeobox leucine zipper proteins HAT4 and HAT5, homeodomain transcription factor–like protein, CONSTANS-like B box zinc finger protein–like protein, abscisic acid–responsive element binding factor, homeobox protein
 Uniquitin-proteasome
 pathway166 polyuniquitin and ubiquitin genes, 2 26S proteasome subunits, 5 E2 and 3 E3 genes
  • a PSI and PSII, photosystems I and II; Rubisco, ribulose-1,5-bisphosphate carboxylase/oxygenase; GST, glutathione S-transferase; ACC, 1-aminocyclopropane-1-carboxylic acid; SAM, S-adenosyl methionine.