Table 2.
Genes highly down-regulated in nodules after extended dark periods.
| Gene | Lotus gene ID | Expression ratio versus control | P-value | |
|---|---|---|---|---|
| 24h/N. Ph. | 72h/N. Ph. | |||
| Starch metabolism | ||||
| Soluble starch synthase {Arabidopsis thaliana} | TC15963 | 0.34 | 0.17 | 0.024 |
| ADP-glucose pyrophosphorylase small subunit PvAGPS1 | TC8396 5 end | 0.08 | 0.02 | 0.004 |
| ADP-glucose pyrophosphorylase small subunit CagpS1 | TC8756 3 end | 0.06 | 0.03 | 0.011 |
| Other carbohydrate metabolism | ||||
| Trehalose-6-phosphate synthase homologue | TC14996 | 0.12 | 0.03 | 0.004 |
| Phosphoglucomutase, cytoplasmic | TC14676 | 0.14 | 0.09 | 0.025 |
| Phosphoglucomutase, cytoplasmic | TC14675 | 0.40 | 0.07 | 0.036 |
| Glucose-6-phosphate isomerase | TC17137 | 0.28 | 0.20 | 0.033 |
| Sucrose synthase 1 | TC7847 | 0.16 | 0.08 | 0.004 |
| Glycolysis | ||||
| Enolase | TC14118 | 0.36 | 0.13 | 0.004 |
| Enolase | TC16760 | 0.73 | 0.17 | 0.004 |
| Pyruvate decarboxylase II | TC7922 | 0.27 | 0.17 | <0.001 |
| Pentose phosphate pathway | ||||
| Glucose-6-phosphate 1-dehydrogenase | TC8851 | 0.29 | 0.06 | 0.004 |
| Transaldolase | TC11589 | 0.02 | 0.01 | 0.011 |
| Transaldolase ToTAL2 | TC10369 | 0.18 | 0.08 | 0.011 |
| TCA cycle | ||||
| Cytosolic malate dehydrogenase (1.1.1.37) | TC7834 | 0.28 | 0.15 | 0.011 |
| Aconitate hydratase, cytoplasmic | TC14371 | 0.37 | 0.16 | 0.004 |
| CO2 metabolism | ||||
| Carbonic anhydrase LjCA1 | TC14306 | 0.01 | 0.00 | 0.004 |
| CA α-type | Ljnest13e5 | 0.33 | 0.13 | <0.001 |
| CA α-type 2 | Ljnest20a7rc | 0.20 | 0.08 | 0.004 |
| Phosphoenolpyruvate carboxylase | TC7830 | 0.60 | 0.11 | 0.009 |
| Phosphoenolpyruvate carboxylase kinase | TC14602 | 0.19 | 0.07 | 0.004 |
| Ribulose bisphosphate carboxylase/oxygenase activase | TC14081 | 0.17 | 0.03 | 0.012 |
| Ammonium assimilation | ||||
| Glutamine synthetase, cytosolic isozyme | TC8035 | 0.39 | 0.13 | 0.007 |
| Glutamate dehydrogenase | TC10844 | 0.20 | 0.16 | 0.008 |
| Other aminoacid metabolism | ||||
| Alanine:glyoxylate aminotransferase 2 homologUE | TC9107 | 0.48 | 0.10 | 0.016 |
| Histidinol dehydrogenase | TC10151 | 0.17 | 0.06 | 0.004 |
| Serine acetyltransferase | TC17048 | 0.19 | 0.05 | 0.004 |
| Cysteine synthase | TC14692 | 0.15 | 0.08 | 0.011 |
| Plastidic cysteine synthase 1 | TC17110 | 0.03 | 0.07 | <0.001 |
| Threonine dehydratase/deaminase | TC18952 | 0.20 | 0.17 | <0.001 |
| Aspartokinase-homoserine dehydrogenase (HDH) | TC9572 | 0.07 | 0.01 | 0.004 |
| Threonine synthase | TC9527 | 0.20 | 0.07 | 0.004 |
| Pantoate-beta-alanine ligase | TC12836 | 0.19 | 0.14 | <0.001 |
| Similarity to ornithine cyclodeaminase | TC11292 | 0.23 | 0.08 | 0.001 |
| Prolyl 4-hydroxylase | TC15896 | 0.29 | 0.11 | <0.001 |
| Prolyl 4-hydroxylase, alpha subunit-like protein | TC11925 | 0.32 | 0.20 | 0.005 |
| Branched-chain amino acid aminotransferase-like protein | TC16062 | 0.13 | 0.01 | 0.004 |
| Other metabolism | ||||
| Chalcone reductase | TC8351 | 0.01 | 0.00 | 0.011 |
| Putative flavanone 3-hydroxylase | TC7931 | 0.40 | 0.14 | 0.004 |
| Acidic endochitinase | TC14167 | 0.16 | 0.04 | <0.001 |
| Thiazole biosynthetic enzyme precursor | TC14068 | 0.06 | 0.02 | 0.004 |
| Cytochrome P450 | TC15466 | 0.33 | 0.04 | 0.004 |
| Cytochrome P450 | TC8343 | 0.05 | 0.01 | <0.001 |
| N-Hydroxycinnamoyl/benzoyltransferase-like protein | TC8570 | 0.23 | 0.08 | 0.004 |
| Isoliquiritigenin 2’-O-methyltransferase | TC14525 | 0.35 | 0.17 | <0.001 |
| 4-Coumarate:CoA ligase 2 | TC7977 | 0.47 | 0.16 | 0.003 |
| Laccase | TC17617 | 0.04 | 0.02 | 0.025 |
| Pyrroline-5-carboxylate reductase | TC15604 | 0.25 | 0.17 | <0.001 |
Gene expression in L. japonicus nodules harvested from plants grown under normal photoperiod (N. Ph.), or subjected to 24h and 72h continuous darkness, respectively. Transcript levels of these genes decreased significantly (<5-fold, P < 0.05) under extended dark conditions and are marked in bold. The numbers indicate ratios of gene expression after 24h and 72h continuous darkness versus expression in the normal photoperiod (control). The P-value represents the level of significance between the relative gene expression levels (ANOVA).