Table 2. Differentially expressed proteins in Persicaria minor leaf proteome upon methyl jasmonate (MeJA) treatment.
Mean peak areas (three biological replicates) for control (Mean C) and treated (Mean T) samples were generated from SWATH-MS proteomics analysis. Differentially expressed proteins were selected based on three statistical analyses detailed in Methods (p < 0.05) as well as having normalized fold change (FC.norm) of control over treated samples greater than 1.5 (significantly up-regulated proteins) or lesser than 0.67 (significantly down- regulated proteins). Protein ID, protein name, UniProt accession number and organism were retrieved from the protein annotation of the P. minor transcriptome (Rahnamaie-Tajadod et al., 2017). Please refer to Tables S4 and S5 for detailed descriptions of the raw data and analyses performed.
| Protein ID | Mean C | Mean T | FC.norm | Protein name | UniProt accession # | Organism |
|---|---|---|---|---|---|---|
| Significantly up-regulated proteins upon MeJA treatment | ||||||
| Proteinase inhibitors | ||||||
| cds.c56865_g2_i9—m.103397 | 376,975.69 | 1,737,837.61 | 6.87 | Proteinase inhibitor | P82381 | Linum usitatissimum |
| cds.c56865_g2_i6—m.103394 | 1,555,104.16 | 5,873,182.80 | 5.58 | Proteinase inhibitor | P82381 | Linum usitatissimum |
| cds.c56865_g2_i3—m.103392 | 1,473,435.88 | 4,406,842.71 | 4.44 | Proteinase inhibitor | P82381 | Linum usitatissimum |
| cds.c56865_g2_i7—m.103395 | 2,574,250.57 | 3,654,504.10 | 2.08 | Proteinase inhibitor | P82381 | Linum usitatissimum |
| Redox processes | ||||||
| cds.c55935_g2_i2—m.93522 | 175,025.05 | 668,494.17 | 5.37 | Peroxidase 12 | Q96520 | Arabidopsis thaliana |
| cds.c55935_g2_i6—m.93526 | 1,385,492.12 | 1,962,003.60 | 2.09 | Peroxidase 12 | Q96520 | Arabidopsis thaliana |
| cds.c51696_g2_i3—m.56033 | 2,223,906.61 | 3,067,324.59 | 2.03 | Peroxidase 12 | Q96520 | Arabidopsis thaliana |
| cds.c55509_g2_i1—m.89283 | 2,093,087.19 | 2,810,777.22 | 2.00 | Peroxidase 12 | Q96520 | Arabidopsis thaliana |
| cds.c48482_g2_i8—m.34843 | 1,360,455.24 | 1,524,257.70 | 1.63 | Peroxidase 51 | Q9SZE7 | Arabidopsis thaliana |
| cds.c48482_g4_i2—m.34836 | 1,137,963.39 | 1,243,194.77 | 1.58 | Peroxidase 51 | Q9SZE7 | Arabidopsis thaliana |
| cds.c44085_g1_i1—m.17116 | 98,123.59 | 103,360.01 | 1.57 | Thioredoxin O1 | O64764 | Arabidopsis thaliana |
| Photosynthesis | ||||||
| cds.c54051_g1_i9—m.75181 | 4449.63 | 15,270.92 | 5.28 | Carbonic anhydrase 2 | P42737 | Arabidopsis thaliana |
| Proteases | ||||||
| cds.c54084_g3_i17—m.75490 | 73,270.41 | 130,253.17 | 2.59 | Serine carboxypeptidase-like 18; | Q9C7Z9 | Arabidopsis thaliana |
| cds.c56708_g2_i3—m.101695 | 158,802.63 | 22,1382.40 | 2.06 | Serine carboxypeptidase-like 17 | Q9C7D6 | Arabidopsis thaliana |
| cds.c56645_g8_i5—m.101004 | 305,355.00 | 317,549.28 | 1.54 | Aspartic proteinase A1 | O65390 | Arabidopsis thaliana |
| Lipid metabolism | ||||||
| cds.c55798_g3_i4—m.92174 | 46,335.46 | 80,368.30 | 2.27 | Linoleate 13S-lipoxygenase 2-1 | O24370 | Solanum tuberosum |
| cds.c48157_g2_i2—m.33078 | 44,999.96 | 62,352.04 | 2.03 | GDSL esterase/lipase | Q9LY84 | Arabidopsis thaliana |
| Phenolic biosynthesis | ||||||
| cds.c55964_g4_i8—m.93866 | 898,732.36 | 1,260,712.36 | 2.04 | Flavanone-3-hydroxylase | Q06942 | Malus domestica |
| cds.c48582_g2_i1—m.35349 | 54,305.20 | 58,084.49 | 1.59 | Chorismate mutase 1 | P42738 | Arabidopsis thaliana |
| Aromatic compound biosynthesis | ||||||
| cds.c56987_g1_i3—m.104679 | 303,398.86 | 329,336.50 | 1.54 | Enone oxidoreductase | K4BW79 | Solanum lycopersicum |
| Protein glycosylation | ||||||
| cds.c50257_g2_i3—m.45689 | 2,777.00 | 3,317.73 | 1.86 | Beta-hexosaminidase 1 | A7WM73 | Arabidopsis thaliana |
| Nitrogen storage | ||||||
| cds.c51882_g2_i1—m.57255 | 5,854,784.07 | 7,322,486.75 | 1.84 | Bark storage protein A (BSPA) | Q07469 | Populus deltoides |
| DNA binding/processing | ||||||
| cds.c46849_g1_i2—m.26698 | 245,864.94 | 294,842.61 | 1.83 | MFP1 (Matrix Attachment Region binding filament-like protein) attachment factor 1 (MAF1) | Q9M7N6 | Solanum lycopersicum |
| cds.c45380_g1_i1—m.20949 | 441,316.13 | 47,1058.03 | 1.62 | Ubiquitin-conjugating enzyme E2 variant 1D | Q9SVD7 | Arabidopsis thaliana |
| cds.c55178_g1_i9—m.85889 | 166,317.71 | 177,336.50 | 1.57 | Endonuclease 4 | F4JJL0 | Arabidopsis thaliana |
| Cell wall degradation | ||||||
| cds.c57837_g2_i2—m.114445 | 64,963.22 | 76,742.82 | 1.70 | α-L-arabinofuranosidase 1 (ARAF1) | Q9SG80 | Arabidopsis thaliana |
| Cofactor biosynthesis | ||||||
| cds.c52258_g2_i5—m.60154 | 4,321,984.23 | 4,568,443.02 | 1.55 | FO synthase | Q5YQD7 | Nocardia farcinica |
| Unknown | ||||||
| cds.c42560_g3_i2—m.13863 | 413,951.96 | 426,939.66 | 1.54 | Uncharacterized protein | Q9ZUX4 | Arabidopsis thaliana |
| Significantly down-regulated proteins upon MeJA treatment | ||||||
| Protein synthesis/modification | ||||||
| cds.c49616_g1_i1—m.41564 | 3,013,895.02 | 1,408,517.22 | 0.66 | Elongation factor-Tu | P46280 | Glycine max |
| cds.c44545_g1_i1—m.18392 | 168,891.20 | 54,051.02 | 0.44 | Probable deoxyhypusine synthase | Q9YE72 | Aeropyrum pernix |
| Photosynthesis | ||||||
| cds.c56271_g1_i1—m.97063 | 585,856.87 | 265,127.66 | 0.66 | ATP-dependent zinc metalloprotease FTSH 8 | Q8W585 | Arabidopsis thaliana |
| cds.c54200_g1_i2—m.76520 | 2,163,792.92 | 954,822.57 | 0.65 | Protein translocon at the inner envelope membrane of chloroplasts (TIC) 62 | Q8SKU2 | Pisum sativum |
| cds.c52014_g2_i2—m.58176 | 585,776.63 | 254,375.22 | 0.61 | chloroplast stem-loop binding protein of 41 kDa b | Q9SA52 | Arabidopsis thaliana |
| cds.c52536_g1_i1—m.62408 | 577,417.30 | 176,611.11 | 0.48 | Rhodanese-like domain-containing protein 4 | Q9M158 | Arabidopsis thaliana |
| cds.c54808_g4_i1—m.82256 | 742,278.68 | 228,493.84 | 0.45 | ATP-dependent zinc metalloprotease FTSH 1 | Q5Z974 | Oryza sativa |
| cds.c49073_g3_i3—m.38259 | 748,656.47 | 194,635.44 | 0.38 | Glycerate dehydrogenase | P13443 | Cucumis sativus |
| rRNA processing | ||||||
| cds.c57862_g3_i2—m.114731 | 199,431.98 | 85,355.50 | 0.65 | Pescadillo homolog | A4RLI4 | Magnaporthe oryzae |
| Structure | ||||||
| cds.c53365_g2_i1—m.69332 | 383,685.96 | 148,936.95 | 0.54 | Tubulin beta-2 chain | Q40106 | Lupinus albus |
| Transcription factor | ||||||
| cds.c37568_g1_i1—m.8344 | 102,097.61 | 37,178.92 | 0.53 | Transcription factor GATA-6 | P43693 | Gallus gallus |
| Unknown | ||||||
| cds.c54200_g3_i1—m.76523 | 399,079.08 | 160,138.06 | 0.60 | Unknown protein | – | – |