Number of Clones Involved in Different Functional Groups Upregulated or Downregulated at Least Two-Fold by White Light
| Pathways | Gene Number | Representative Gene Namesa |
|---|---|---|
| Upregulated | ||
| Photosynthetic light reactions | 56 | 17 CAB genes, 15 PSI proteins, 14 PSII proteins, 10 proteins involved in electron transport and ATP synthesis |
| Photosynthetic carbon metabolism | 25 | 4 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 synthesis | 3 | Fructose-1,6-bisphosphate aldolase, fructose-1,6-bisphosphate phosphatase, pyrophosphorylase |
| Sucrose synthesis | 5 | Phosphate/triose phosphate translocator, cytosolic triose-phosphate isomerase, cytosolic fructose-1,6-bisphosphate aldolase, phosphofructokinase, sucrose synthase |
| Photorespiration | 8 | 4 RBCS genes, glycolate oxidase, catalase, hydroxypyruvate reductase, glycine decarboxylase |
| Glycolysis | 5 | Fructokinase, triose phosphate isomerase, pyruvate kinase, pyruvate decarboxylase, alcohol dehydrogenase |
| Trichloroacetic acid cycle | 5 | Pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, phosphopyruvate hydratase, malate dehydrogenase |
| Cell wall synthesis and cell wall protein | 8 | Cellulose synthase, glucosyltransferase, β-1,2-xylosyltransferase, UDP-glucose:glycoprotein glucosyltransferase, cell wall–plasma membrane linker protein, proline-rich protein, extensin, AGP |
| Protein synthesis in chloroplast | 56 | 11 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 cytoplasm | 60 | 15 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 biosynthesis | 8 | PAL1, CHS, caffeoyl-CoA O-methyltransferase, cinnamyl-alcohol dehydrogenase, O-methyltransferase, GST, glutathione-conjugate transporters, cytochrome P450 |
| Amino acid synthesis pathways | 15 | Dehydrogenase, 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 synthesis | 4 | Ferrochelatase, glutamyl-tRNA reductase, protoporphyrinogen IX oxidase, glutamate-1-semialdehyde 2,1-aminomutase 1 |
| Transcription factors | 15 | G-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 pathway | 23 | 4 polyuniquitin and ubiquitin genes, 9 26S proteasome subunits, 2 proteasome subunit–related proteins, E1, E2, and 6 E3 genes |
| Downregulated | ||
| Ethylene biosynthesis | 3 | ACC synthase, ACC oxidase, SAM synthase |
| BR biosynthesis | 4 | 24-sterol C-methyltransferase, C-8,7-sterol isomerase, 3-β-hydroxysteroid dehydrogenases, steroid sulfotransferase |
| Cell wall degradation and cell wall proteins | 26 | Cellulase, 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 tonoplast | 5 | 5 aquaporins in tonoplast |
| Water transport across plasma membrane | 5 | 5 water channel and membrane intrinsic proteins in plasma membrane |
| Sulfur assimilation | 9 | 2 GSTs, sulfate adenylyltransferase, sulfate transporter, phytochelatin synthase, cysteine synthase, cytochrome P450 monooxygenase, 2 ABC transporters |
| Nitrogen assimilation | 9 | 3 nitrate transporters, 2 AS proteins, glutamine synthetase, glutamate dehydrogenase, serine carboxypeptidase, cysteine synthase |
| Fatty acid oxidation | 5 | Glycerol-3-phosphate dehydrogenase, inorganic pyrophosphatase, ketoacyl-CoA thiolase, malic enzyme, acyl-CoA oxidase |
| Glyoxylate cycle | 4 | isocitrate lyase, citrate synthase, malate synthase, malate dehydrogenase |
| Transcription factors | 18 | 3 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 pathway | 16 | 6 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.