Table I. Proteins showing higher abundance in HP compared with wild-type plants.
After preparative 2D electrophoresis, differentially expressed proteins were identified by electrospray ionization-MS. Spot identifiers correspond to those indicated in Supplemental Figure S9. Expression ratio is given as the ratio (HP to wild type) of protein abundance as determined by 2D-DIGE analysis (Fig. 6). For each spot, the identity of the protein(s) it contained is indicated by the locus identifier(s) in the tomato genome (http://solgenomics.net/organism/Solanum_lycopersicum/genome) and the corresponding annotation. Protein identifications were accepted only if they could be established at greater than 99% probability and contained at least two peptides, each identified at greater than 95% probability (for details, see Supplemental Methods S1). If multiple spots were identified as isoforms of the same protein (spot count > 1), the given spot identifier corresponds to the spot with the largest difference in expression. Proteins that were less abundant in HP lines compared with wild-type plants are shown in Supplemental Table S1.
| Spot Identifier | Spot Count | Ratio | Locus | Solanaceae Genomics Network Annotation |
|---|---|---|---|---|
| 6006 | 7 | 57.1 | Solyc08g079870 | Subtilisin-like protease (P69B) |
| 5656 | 1 | 28.5 | Solyc08g008210 | V-type proton ATPase subunit E |
| Solyc06g081980 | Pyridoxyl biosynthesis lyase pdx6 | |||
| 5826 | 2 | 12.7 | Solyc09g090980 | Major allergen Mal d 1 (PR-10) |
| 5671 | 1 | 9.6 | Solyc10g055810 | Endochitinase (PR-3) |
| 5827 | 1 | 7.3 | Solyc01g079820 | Redoxin domain protein |
| 5816 | 1 | 6.1 | Solyc01g100030 | Deoxyuridine 5′-triphosphate nucleotide hydrolase (dUTPase) |
| 5644 | 2 | 5.2 | Solyc07g051850 | Aspartic proteinase (cyprosin-like) |
| 5909 | 1 | 4.3 | Solyc00g174340 | Pathogenesis-related protein 1b (PR-1b) |
| 5642 | 1 | 3.6 | Solyc08g080140 | dTDP-4-dehydrorhamnose reductase |
| 6015 | 1 | 3.4 | Solyc11g069270 | β-Galactosidase |
| 5731 | 1 | 3.2 | Solyc01g088480 | Adenylate kinase |
| 5587 | 1 | 3.2 | Solyc05g052600 | Fru-1,6-bisphosphatase class 1 |
| 6025 | 2 | 3.1 | Solyc06g073190 | Fructokinase |
| Solyc09g082060 | Cys synthase | |||
| 6183 | 5 | 3.0 | Solyc07g052350 | 3-Isopropylmalate dehydratase large subunit (aconitate hydratase) |
| 5273 | 1 | 2.8 | Solyc05g050970 | Transketolase1 |
| 5271 | 1 | 2.5 | Solyc08g079170 | Stress-induced protein, sti1-like protein |
| 5696 | 1 | 2.3 | Solyc03g025850 | Remorin1 |
| 6040 | 1 | 2.1 | Solyc05g054760 | Dehydroascorbate reductase |
| 5593 | 1 | 2.1 | Solyc05g014470 | Glycerinaldehyde-3-phosphate dehydrogenase |
| 6144 | 1 | 2.0 | Solyc03g123830 | Phosphoglycerate dehydrogenase |
| Solyc04g045340 | Phosphoglucomutase |