Table 1.
Differentially expressed proteins identified in control and Cu‐treated R. mucilaginosa cells
| Spot no.a | Protein name | Accession no. (gi) | Predicted Mr/pI | Observed Mr/pI | Number of matched peptides | Reference species | Protein score | Protein score C.I.% | Fold change b | p‐value |
|---|---|---|---|---|---|---|---|---|---|---|
| Carbohydrate and energy metabolism | ||||||||||
| 109 | L‐malate dehydrogenase, mitochondrial | 472581873 | 35.58/8.76 | 34.27/6.58 | 5 | Rhodosporidium toruloides | 77 | 98.17 | 0.086 | 0.01 |
| 220 | L‐malate dehydrogenase, mitochondrial | 472581873 | 35.58/8.76 | 37.06/6.87 | 5 | Rhodosporidium toruloides | 205 | 100.00 | 0.056 | 0.00 |
| 221 | Alcohol dehydrogenase | 472587838 | 38.20/6.46 | 42.26/6.87 | 5 | Rhodosporidium toruloides | 109 | 100.00 | + | 0.01 |
| 605 | 6‐Phosphogluconate dehydrogenase | 472587565 | 52.44/6.21 | 58.32/6.73 | 10 | Rhodosporidium toruloides | 98 | 99.98 | 0.086 | 0.00 |
| 701 | NADH dehydrogenase (ubiquinone) flavoprotein 1 | 472584566 | 56.55/8.16 | 62.03/6.88 | 12 | Rhodosporidium toruloides | 242 | 100.00 | 0.083 | 0.01 |
| 702 | 6‐Phosphogluconate dehydrogenase | 472587565 | 52.44/6.21 | 62.06/6.77 | 9 | Rhodosporidium toruloides | 85 | 99.74 | 0.080 | 0.01 |
| 1502 | 2‐Methylcitrate synthase | 472580577 | 21.99/8.67 | 48.67/6.62 | 3 | Rhodosporidium toruloides | 73 | 95.23 | 10.65 | 0.02 |
| 3402 | Pyruvate dehydrogenase E1 component subunit alpha | 472583762 | 47.58/8.09 | 46.23/6.18 | 9 | Rhodosporidium toruloides | 264 | 100.00 | 0.092 | 0.00 |
| 3408 | Pyruvate dehydrogenase E1 component subunit alpha | 472583762 | 47.58/8.09 | 45.29/6.16 | 9 | Rhodosporidium toruloides | 172 | 100.00 | 12.38 | 0.01 |
| 3502 | Dihydrolipoyl dehydrogenase | 472585468 | 52.44/6.81 | 55.68/6.14 | 13 | Rhodosporidium toruloides | 245 | 100.00 | 0.096 | 0.01 |
| 3715 | NADH dehydrogenase (ubiquinone) Fe‐S protein 1 | 472583921 | 81.76/7.21 | 76.31/5.66 | 15 | Rhodosporidium toruloides | 190 | 100.00 | + | 0.02 |
| 4104 | Phosphoglycerate mutase 1 | 472585349 | 24.39/6.68 | 26.31/5.76 | 6 | Rhodosporidium toruloides | 178 | 100.00 | ‐ | 0.03 |
| 4408 | 3‐Deoxy‐8‐phosphoheptulonate synthase | 472582537 | 40.00/6.42 | 45.37/5.63 | 4 | Rhodosporidium toruloides | 77 | 98.23 | 11.34 | 0.01 |
| 4709 | Oxoglutarate dehydrogenase | 342320257 | 127.33/6.01 | 94.28/5.46 | 8 | Rhodotorula glutinis | 149 | 100.00 | + | 0.02 |
| 5607 | UDP‐galactopyranose mutase | 472586186 | 56.29/6.05 | 63.22/5.42 | 4 | Rhodosporidium toruloides | 79 | 98.76 | 0.026 | 0.00 |
| 6508 | Enolase | 501310447 | 46.36/5.14 | 50.10/5.12 | 1 | Pseudozyma hubeiensis | 84 | 99.62 | 12.65 | 0.01 |
| 5706 | Pyruvate kinase | 472583934 | 56.42/6.30 | 60.15/5.23 | 6 | Rhodosporidium toruloides | 169 | 100.00 | 13.15 | 0.01 |
| 6603 | 2‐Isopropylmalate synthase | 342320438 | 67.90/5.89 | 59.18/5.18 | 8 | Rhodotorula glutinis | 175 | 100.00 | ‐ | 0.01 |
| 6711 | Pyruvate dehydrogenase E2 component | 472582629 | 61.32/6.52 | 61.85/5.02 | 12 | Rhodosporidium toruloides | 139 | 100.00 | + | 0.00 |
| 6914 | Glycerol‐3‐phosphate dehydrogenase | 342318964 | 147.96/8.64 | 129.87/5.21 | 12 | Rhodotorula glutinis | 128 | 100.00 | + | 0.03 |
| 7404 | Enolase | 1022840960 | 47.78/5.33 | 46.58/5.21 | 4 | Rhodosporidium toruloides | 77 | 98.25 | 0.090 | 0.00 |
| 7806 | Glycogen phosphorylase | 517243372 | 92.34/5.80 | 86.43/5.26 | 18 | Burkholderia sp. | 75 | 97.23 | 35.05 | 0.01 |
| 8102 | Transaldolase | 472586368 | 35.80/5.67 | 34.57/4.92 | 6 | Rhodosporidium toruloides | 142 | 100.00 | 0.078 | 0.01 |
| 8202 | 6‐Phosphogluconate dehydrogenase | 472587565 | 52.44/6.21 | 45.13/4.96 | 9 | Rhodosporidium toruloides | 77 | 98.25 | ‐ | 0.01 |
| 8209 | Pyruvate dehydrogenase E1 component subunit beta | 472585974 | 42.92/5.74 | 46.19/4.62 | 4 | Rhodosporidium toruloides | 87 | 99.84 | 0.070 | 0.02 |
| 9302 | Pyruvate dehydrogenase E1 component subunit beta | 472585974 | 42.92/5.74 | 47.08/4.63 | 6 | Rhodosporidium toruloides | 70 | 90.18 | 0.086 | 0.00 |
| Protein folding | ||||||||||
| 2714 | Heat shock protein 70, hsp70A2 | 172718 | 70.50/5.05 | 69.82/5.89 | 11 | Saccharomyces cerevisiae | 269 | 100.00 | + | 0.01 |
| 3003 | NB‐ARC and TPR repeat‐containing protein | 298714756 | 164.84/5.44 | 20.58/5.88 | 6 | Ectocarpus siliculosus | 73 | 95.90 | 14.31 | 0.01 |
| 3716 | Heat shock protein/chaperonin | 472585379 | 89.72/6.11 | 85.63/6.14 | 8 | Rhodosporidium toruloides | 106 | 100.00 | + | 0.03 |
| 5703 | T‐complex protein 1 subunit beta | 472580721 | 56.46/5.70 | 70.46/5.42 | 12 | Rhodosporidium toruloides | 99 | 99.99 | 12.34 | 0.00 |
| 7006 | 70 kDa heat shock protein | 171728 | 69.61/5.03 | 24.88/4.89 | 9 | Saccharomyces cerevisiae | 113 | 100.00 | 0.054 | 0.01 |
| 7407 | Heat shock protein 70 | 562977171 | 70.19/5.03 | 42.73/4.85 | 8 | Ogataea parapolymorpha | 232 | 100.00 | 0.082 | 0.03 |
| 7701 | Molecular chaperone DnaK | 472580771 | 70.79/5.96 | 80.21/5.23 | 10 | Rhodosporidium toruloides | 322 | 100.00 | 0.066 | 0.02 |
| 7707 | Heat shock protein 70A2 | 172718 | 70.50/5.05 | 80.23/5.11 | 12 | Saccharomyces cerevisiae | 217 | 100.00 | 0.026 | 0.02 |
| 8311 | Heat shock protein 70 | 1708305 | 70.09/5.11 | 40.22/4.61 | 10 | Ogataea angusta | 124 | 100.00 | 0.054 | 0.01 |
| Nucleotide and protein metabolism | ||||||||||
| 302 | Elongation factor EF‐1 alpha subunit | 472587418 | 50.17/9.15 | 47.21/6.98 | 6 | Rhodosporidium toruloides | 77 | 98.29 | 23.23 | 0.00 |
| 304 | Elongation factor EF‐1 alpha subunit | 472587418 | 50.17/9.15 | 48.09/6.84 | 9 | Rhodosporidium toruloides | 162 | 100.00 | ‐ | 0.02 |
| 314 | ATP‐dependent RNA helicase RhlE | 491634597 | 51.03/9.90 | 52.03/6.80 | 8 | Pseudoalteromonas luteoviolacea | 77 | 98.29 | + | 0.01 |
| 507 | Elongation factor EF‐1 alpha subunit | 472587418 | 50.17/9.15 | 48.92/6.43 | 9 | Rhodosporidium toruloides | 113 | 100.00 | + | 0.01 |
| 3509 | IMP dehydrogenase | 472580737 | 56.86/6.44 | 55.63/5.89 | 3 | Rhodosporidium toruloides | 104 | 100.00 | 0.052 | 0.03 |
| 5614 | Elongation factor EF‐1 alpha subunit | 472587418 | 50.17/9.15 | 56.28/5.38 | 6 | Rhodosporidium toruloides | 73 | 95.51 | 15.43 | 0.02 |
| 6203 | Translation initiation factor eIF‐3 subunit 2 | 472585701 | 38.44/5.51 | 37.28/5.21 | 4 | Rhodosporidium toruloides | 105 | 100.00 | 0.086 | 0.01 |
| 7002 | Putative chromatin remodeling complex atpase chain isw1 protein | 485924588 | 127.25/5.99 | 24.38/5.21 | 8 | Neofusicoccum parvum | 74 | 96.27 | 0.084 | 0.01 |
| 8701 | SARP family transcriptional regulator | 517739234 | 123.61/5.86 | 79.63/4.89 | 13 | Salinispora arenicola | 73 | 95.71 | ‐ | 0.00 |
| 8803 | Single‐stranded DNA binding protein | 472580369 | 55.95/5.03 | 101.23/5.01 | 7 | Rhodosporidium toruloides | 88 | 99.86 | 52.56 | 0.03 |
| Antioxidative system | ||||||||||
| 2002 | Mitochondrial peroxiredoxin 6, 1‐Cys peroxiredoxin | 472586343 | 24.95/5.86 | 23.43/6.02 | 4 | Rhodosporidium toruloide | 74 | 96.27 | 12.81 | 0.01 |
| 4108 | Catalase A | 472584117 | 87.82/6.21 | 25.68/5.42 | 7 | Rhodosporidium toruloides | 133 | 100.00 | ‐ | 0.02 |
| 5109 | Mitochondrial peroxiredoxin 6, 1‐Cys peroxiredoxin | 472586343 | 24.95/5.86 | 26.48/5.39 | 4 | Rhodosporidium toruloides | 152 | 100.00 | 12.88 | 0.01 |
| Signaling | ||||||||||
| 5202 | 3‐beta hydroxysteroid dehydrogenase/isomerase | 472581852 | 37.06/5.81 | 37.23/5.41 | 7 | Rhodosporidium toruloides | 91 | 99.93 | 0.080 | 0.02 |
| Unknown function | ||||||||||
| 8607 | Hypothetical protein GUITHDRAFT_161407 | 428182889 | 49.42/6.54 | 54.21/4.43 | 16 | Guillardia theta | 80 | 99.00 | 0.090 | 0.01 |
| 2004 | hypothetical protein HMPREF1120_08112 | 378733681 | 185.26/5.12 | 25.24/6.02 | 7 | Exophiala dermatitidis | 74 | 96.27 | 21.46 | 0.01 |
a
Spot number corresponds to the 2‐DE imagines in Figure 9a and b.
b
Fold change is the ratio between average volume of each protein spots in Cu‐treated cells compared control cells. If the ratio is higher than 10‐fold, it is accepted as upregulation; if it is lower than 0.1‐fold, it is accepted as downregulation. “+/−” means that the protein was appeared/disappeared in copper‐induced cells.