Table 3.
Genes up-regulated in P. cheesemanii, P. exile and P. novae-zelandiae in transcript and protein profiling
| T | P | T | P | ||||
|---|---|---|---|---|---|---|---|
| Locus | Description | LogFC | LogFC | Locus | Description | LogFC | LogFC |
| P. cheesemanii (29 genes up-regulated) | P. cheesemanii (2 genes down-regulated) | ||||||
| Translation | Cell wall modification | ||||||
| At1g05190 | ribosomal protein L6 | 1.6 | 1.6 | At1g11580 | pectin methylesterase | -1.1 | -1 |
| At3g02560 | 40S ribosomal protein S7 | 1.0 | 2.9 | Carbohydrate metabolism | |||
| At5g13510 | ribosomal protein L10 family protein | 1.0 | 1.7 | At4g19810 | glycosyl hydrolase family 18 protein | -0.8 | -1.4 |
| At5g30510 | 30S ribosomal protein S1 | 1.5 | 1.9 | ||||
| At5g54600 | 50S ribosomal protein L24 | 0.8 | 3.7 | P. exilis (4 genes up-regulated) | |||
| Photosynthesis light phase | Citrate cycle | ||||||
| At1g52230 | photosystem I subunit H2 | 2.4 | 2.3 | At2g20420 | succinyl-CoA ligase (GDP-forming) beta | 0.7 | 0.9 |
| At4g21280 | photosystem II subunit Q | 1.2 | 1.8 | S-adenosylmethionine biosynthetic process | |||
| At4g03280 | Rieske FeS center of cytochrome b6f | 1.2 | 1.2 | At2g36880 | methionine adenosyl transferase 3 | 0.7 | 1.2 |
| At5g64040 | photosystem I subunit N | 1.8 | 4.7 | Carbohydrate metabolism | |||
| At4g04640 | chloroplast ATP synthase gamma subunit | 1.3 | 0.8 | At5g11720 | alpha-glucosidase 1 | 0.7 | 5.0 |
| At3g01480 | chloroplast cyclophilin | 1.3 | 2.0 | Other | |||
| Calvin cycle | At4g34180 | cyclase family protein | 0.9 | 1.6 | |||
| At1g12900 | gap dehydrogenase a subunit 2 | 1.7 | 0.6 | ||||
| At1g32060 | phosphoribulokinase (PRK) | 1.5 | 0.6 | P. exilis (4 genes down-regulated) | |||
| Pentose phosphate pathway | Carbohydrate metabolism | ||||||
| At2g21330 | fructose-bisphosphate aldolase 1 | 1.3 | 0.4 | At1g70730 | phosphoglucomutase, cytoplasmic | -0.7 | -0.32 |
| Fatty acid beta oxidation | Stress response | ||||||
| At5g09660 | peroxisomal malate dehydrogenase 2 | 1.4 | 1.0 | At3g11930 | universal stress protein (USP) | -2.6 | -2.8 |
| Interconversion of CO2 and bicarbonate | At5g24770 | vegetative storage protein 2 (VSP2) | -2.4 | -3.4 | |||
| At3g01500 | carbonic anhydrase 1, chloroplast | 3.3 | 1.8 | At5g24780 | vegetative storage protein 1 (VSP1) | -2.9 | -3.5 |
| At5g14740 | carbonic anhydrase 2, cytoplasm | 1.4 | 1.2 | ||||
| Protein folding | P. novae-zelandiae (8 genes up-regulated) | ||||||
| At1g55490 | chloroplast chaperonin 60 beta | 0.9 | 1.4 | Detoxification of xenobiotics | |||
| At5g20720 | 20 kDa chaperonin chloroplast | 0.9 | 2.1 | At1g17170 | glutathione S-transferase | 2.7 | 9.7 |
| Oxidative stress | At3g62700 | glutathione-conjugate transporter | 1.2 | 3.2 | |||
| At1g07890 | L-ascorbate peroxidase 1, cytosolic | 0.8 | 0.4 | Cellular metal ion homeostasis | |||
| At5g06290 | 2-cys peroxiredoxin, chloroplast | 1.1 | 1.2 | At4g16370 | oligopeptide transporter family protein | 1.4 | 8.5 |
| Serine family amino acid metabolic process | Interconversion of CO2 and bicarbonate | ||||||
| At4g11640 | serine racemase | 2.3 | 1.6 | At1g23730 | carbonic anhydrase | 1.7 | 4.3 |
| Other | Stress response | ||||||
| At4g02530 | chloroplast thylakoid lumen protein | 1.3 | 3.5 | At5g24770 | vegetative storage protein 2 (VSP2) | 3.5 | 12.1 |
| At1g54780 | thylakoid lumen 18.3 kDa protein | 1.3 | 1.3 | At5g24780 | vegetative storage protein 1 (VSP1) | 2.6 | 6.3 |
| At2g37220 | chloroplast RNA binding protein | 1.0 | 3.7 | At5g58390 | peroxidase | 1.4 | 3.5 |
| At1g57770 | amine oxidase family | 1.1 | 2.2 | Other | |||
| At1g62750 | translation elongation factor | 1.2 | 1.6 | At1g79690 | nudix hydrolase homolog 3 | 0.9 | 2.9 |
| At3g15360 | thioredoxin M-type 4 | 1.5 | 4.6 | ||||
| At5g19440 | alcohol dehydrogenase | 0.9 | 2.2 | ||||
Locus, description, log fold change (logFC), and gene ontology terms (biological process) for genes found specifically up- and down-regulated in P. cheesemanii, P. exile and P. novae-zelandiae when compared to the two remaining species combined. Only genes for which both transcripts (T) and proteins (P) have been found to be differentially expressed are listed (P. cheesemanii: 29 up-regulated genes, 2 down-regulated genes; P. exile: 4 up-regulated genes, 4 down-regulated genes; P. novae-zelandiae: 8 up-regulated genes; compare Venn diagrams in left panel of figure 1).