Table 4.
Proteins identified in two-dimensional IEF–SDS–PAGE. Positive identification was retained with Mascot scores (sco) above the threshold level (P < 0.05), at least two identified peptides with a score (pep/ion) above homology, 10% sequence coverage (%), and similar experimental (exp) and theoretical (th) molecular weight (MW) and pI. Relative spot intensity changes in the WT++ versus WT, atfer1-3-4 versus WT, atfer1-3-4 versus WT, atfer1-3-4++ versus atfer1-3-4, and atfer1-3-4++ versus WT++ comparisons are presented as fold (Student’s t-test, P < 0.1; n=5). Bold and regular characters in fold changes indicate P < 0.05 and 0.05 < P < 0.1, respectively. New and ND indicate spots that have been newly detected or no longer detected, and (–) denotes no significant change. Function was inferred from GO annotation. Spot number (as in Supplementary Fig. 1 at JXB online), UniProt. and AGI codes are shown in columns 1, 2, and 3.
| n | UniProt | AGI code | WT++ versus WT | atfer versus WT | atfer++ versus WT | atfer++ versus atfer | atfer++ versus WT++ | Protein name/function | Sco/pep/ ion | % | MW/pI th | MW/pI exp | Metal binding |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Amino acid metabolism | |||||||||||||
| 1 | O80988 | At2g26080 | – | – | 3.4 | 6.3 | 3.1 | Glycine dehydrogenase 1 | 454/9/9 | 11 | 114.7/6.2 | 111.4/6.2 | |
| 2 | O04130 | At1g17745 | – | – | – | – | 3.0 | d-3-Phosphoglycerate-DH | 625/12/8 | 17 | 66.8/5.8 | 71.3/5.7 | |
| 3 | Q9ZPF5 | At4g08870 | –3.3 | – | – | – | 3.6 | Putative arginase | 834/36/18 | 48 | 38.1/5.9 | 35.4/6.2 | Mn |
| 4 | F4I7I0 | At1g17290 | – | –2.4 | – | – | – | Alanine aminotransferase | 723/15/13 | 28 | 60.4/5.9 | 56.5/5.6 | |
| 5 | P93832 | At1g80560 | – | –2.3 | – | 3.3 | – | 3-Isopropylmalate DH 2 | 607/14/12 | 28 | 43.5/5.8 | 44.3/5.3 | Mn, Mg |
| 6 | Q9SWG0 | At3g45300 | –2.1 | – | – | – | – | Isovaleryl-CoA-DH | 817/22/15 | 33 | 45.4/7.5 | 41.5/6.3 | |
| Protein metabolism/modification | |||||||||||||
| 7 | O24633 | At4g14800 | – | – | – | New | – | Proteasome subunit β type-2-B | 72/2/2 | 14 | 22.1/6.2 | 19.2/6.6 | |
| 8 | Q9LNC1 | At1g06260 | – | – | – | – | 100 | Cysteine proteinase-like protein | 439/12/7 | 28 | 38.3/7.5 | 24.9/4.9 | |
| 9 | C0Z361 | At5g56500 | – | – | 6.6 | – | cpn60 chaperonin family protein | 873/16/14 | 32 | 63.7/5.7 | 65.1/5.6 | ||
| 10 | Q9LKR3 | At5g28540 | – | – | 2.8 | – | – | Heat shock 70kDa protein 11 | 1670/55/30 | 48 | 73.9/5.1 | 81.9/5.3 | |
| 11 | Q43349 | At3g53460 | – | – | 2.6 | – | – | 29kDa ribonucleoprotein | 480/12/8 | 29 | 35.3/5.2 | 28.7/5.0 | |
| 12 | Q9LDZ0 | At5g09590 | – | – | – | 2.3 | – | Heat shock 70kDa protein 10 | 1608/46/28 | 46 | 73.2/5.6 | 73.9/5.5 | |
| 13 | Q9SCX3 | At5g19510 | –25.1 | – | ND | – | – | Elongation factor 1-β2 | 441/12/8 | 41 | 24.2/4.4 | 30.4/4.6 | |
| 14 | O23727 | – | – | –4.6 | – | – | Peptidyl-prolyl cis-trans isomerase | 680/20/12 | 58 | 24.9/5.1 | 27.2/5.2 | ||
| 15 | Q9LY14 | At5g07470 | – | –2.4 | – | – | – | Peptide methionine sulphoxide reductase A3 | 148/5/5 | 21 | 22.8/5.3 | 26.2/5.4 | |
| 16 | O65282 | At5g20720 | – | –2.1 | – | – | – | Chaperonin 10 | 304/6/5 | 19 | 26.9/8.9 | 22.6/5.4 | Cu |
| 17 | O23710 | At3g27430 | – | – | –2.0 | – | – | Proteasome subunit β type-7-A | 322/10/6 | 21 | 29.8/6.7 | 23.4/6.6 | |
| Carbohydrate metabolism | |||||||||||||
| 18 | Q9MA79 | At1g43670 | – | – | New | 4.7 | 4.7 | Fructose-1,6-bisphosphatase | 696/19/12 | 36 | 37.7/5.3 | 39.4/5.6 | Mg |
| 19 | Q9C6Z3 | At1g30120 | – | – | – | 6.9 | – | Pyruvate dehydrogenase E1 β | 260/6/6 | 22 | 44.7/5.9 | 38.6/5.3 | |
| 20 | Q9S7W4 | At3g07720 | – | – | – | 4.4 | 2.7 | Galactose oxidase | 290/5/5 | 18 | 36.0/5.1 | 35.8/5.1 | |
| 21 | Q9SAJ4 | At1g79550 | – | – | 3.8 | – | – | Phosphoglycerate kinase | 908/43/17 | 54 | 42.2/5.5 | 39.2/5.8 | |
| 22 | Q9SAU2 | At5g61410 | – | –4.7 | – | – | – | d-Ribulose-5-P-3-epimerase | 377/16/8 | 29 | 30.1/8.2 | 22.1/6.9 | |
| 23 | Q9M9K1 | At3g08590 | – | –3.9 | – | – | – | Phosphoglyceromutase 2 | 734/16/15 | 41 | 60.9/5.5 | 67.2/6.1 | Mn |
| 24 | Q7DLW9 | – | –3.1 | – | – | – | β-Fructosidase | 669/14/12 | 18 | 73.8/5.4 | 51.7/5.3 | ||
| 25 | Q1WIQ6 | At2g24270 | –2.9 | – | – | – | – | NADP-GAPDH | 470/9/8 | 25 | 53.7/6.2 | 52.7/6.6 | |
| 26 | Q94B07 | –2.7 | – | 3.5 | – | γ Hydroxybutyrate DH | 632/14/12 | 41 | 30.9/5.9 | 28.0/6.1 | |||
| Photosynthesis | |||||||||||||
| 27 | O03042 | AtCg00490 | – | 2.1 | – | – | – | RuBisCO large subunit | 1024/56/19 | 40 | 53.4/5.9 | 54.4/6.2 | Mg |
| 28 | O49292 | At1g77090 | –3.6 | – | – | – | – | OEC23-like protein 5 | 281/4/4 | 22 | 28.7/7.0 | 20.0/6.5 | Ca |
| 29 | Q9ZR03 | At4g03280 | – | – | –2.9 | – | – | Cytochrome b6-f complex Fe–sulphur subunit | 112/3/2 | 10 | 22.8/8.6 | 14.9/6.4 | Fe–S |
| 30 | Q9ZR03 | At4g03280 | – | – | –2.8 | – | – | Cytochrome b6-f complex Fe–sulphur subunit | 513/14/8 | 37 | 24.6/8.8 | 14.1/6.9 | Fe–S |
| 31 | Q42029 | At1g06680 | – | – | –2.5 | – | – | OEC protein 2-1 | 348/17/7 | 32 | 28.2/6.9 | 22.8/6.0 | Ca |
| Cofactor biosynthesis | |||||||||||||
| 32 | Q38814 | At5g54770 | – | – | – | 3.1 | – | Thiamine thiazole synthase | 578/23/7 | 35 | 36.8/5.8 | 31.1/5.5 | Fe |
| 33 | Q38814 | At5g54770 | – | – | – | 2.5 | – | Thiazole biosynthetic enzyme | 645/22/9 | 33 | 36.8/5.8 | 29.6/6.0 | Fe |
| 34 | O48588 | At5g44720 | –5.5 | –6.6 | – | – | – | MOCO sulphurase family protein | 837/27/14 | 44 | 35.0/5.5 | 37.8/5.9 | |
| Lipid metabolism | |||||||||||||
| 35 | O64968 | – | – | – | 2.4 | – | Dihydrolipoylacyltransferase subunit of the AD complex | 866/29/17 | 46 | 53.1/6.3 | 47.5/5.6 | ||
| 36 | Q93YW8 | At4g18970 | – | –24.0 | –5.8 | – | – | GDSL esterase/lipase | 253/13/7 | 19 | 40.1/5.3 | 22.5/6.2 | |
| 37 | Q93YW8 | At4g18970 | – | – | – | – | –2.1 | GDSL esterase/lipase | 403/8/6 | 16 | 70.9/8.2 | 35.2/5.5 | |
| Stress | |||||||||||||
| 38 | Q8LBK6 | At3g15660 | – | –15.4 | –7.3 | – | – | Monothiol glutaredoxin-S15 | 200/7/5 | 38 | 18.8/5.2 | 12.2/4.8 | Fe–S |
| 39 | P28493 | At1g75040 | –4.1 | – | – | – | – | Pathogenesis-related protein 5 | 400/10/8 | 40 | 26.1/4.8 | 25.3/4.7 | |
| 40 | Q96266 | At2g47730 | –6.4 | – | – | – | 6.2 | Glutathione S-transferase-GST6 | 809/51/16 | 62 | 24.1/6.1 | 21.8/6.6 | |
| 41 | Q9SJZ2 | At2g22420 | – | –3.2 | – | 2.2 | – | Peroxidase 17 | 656/15/11 | 41 | 37.1/5.1 | 37.0/5.3 | Fe–haem |
| DNA/RNA processes | |||||||||||||
| 42 | Q03250 | At2g21660 | – | –7.5 | ND | – | – | Glycine-rich RNA-binding protein 7 | 378/9/6 | 43 | 16.9/5.8 | 11.0/6.3 | |
| 43 | Q93W05 | At1g10590 | –6.4 | –3.6 | – | – | – | Replication factor A1 | 322/12/7 | 51 | 15.5/6.6 | 13.3/6.6 | |
| 44 | Q9SMW7 | At1g17880 | – | –2.1 | – | – | – | Basic transcription factor 3 | 249/8/6 | 47 | 17.9/6.6 | 16.0/6.7 | |
| Cell cycle/biogenesis | |||||||||||||
| 45 | Q84M92 | At1g18450 | – | – | – | 2.4 | – | Actin-related protein 4 | 912/20/14 | 47 | 49.4/5.2 | 59.6/5.4 | |
| 46 | P53494 | At5g59370 | – | – | –3.2 | – | – | Actin 4 | 52/2/2 | 12 | 42.0/5.4 | ||
| 47 | Q42545 | At5g55280 | – | –2.4 | – | 3.2 | – | Cell division protein FtsZ 1 | 756/22/14 | 29 | 45.8/6.9 | 36.7/5.2 | |
| Cell wall organization | |||||||||||||
| 48 | Q9LJR7 | At3g25050 | – | – | – | – | 10.4 | Xyloglucan endotransglucosylase hydrolase protein 3 | 253/8/5 | 21 | 33.4/6.0 | 28.4/6.2 | |
| 49 | Q9FLG1 | At5g64570 | – | – | – | ND | β-d-Xylosidase 4 | 522/10/9 | 18 | 85.3/7.8 | 60.4/6.2 | ||
| Secondary metabolism | |||||||||||||
| 50 | P94111 | At1g74020 | – | ND | – | New | – | Strictosidine synthase | 581/14/10 | 41 | 35.6/6.0 | 35.6/6.0 | |
| 51 | Q96330 | At5g08640 | – | – | – | – | 3.6 | Flavonol synthase | 371/11/9 | 37 | 38.3/5.6 | 39.0/5.9 | Fe |
| Others | |||||||||||||
| 52 | O80889 | At2g32520 | – | – | 2.2 | 2.0 | 3.6 | Carboxymethylenebutenolidase | 344/9/6 | 45 | 26.0/5.3 | 24.8/5.4 | Zn stress |
| 53 | Q9FMF2 | –9.4 | – | – | – | – | β-Ureidopropionase | 424/9/6 | 21 | 45.6/6.0 | 43.2/6.5 | ||
| 54 | O64640 | At2g45600 | – | – | –6.7 | – | – | Probable carboxylesterase 8 | 456/11/9 | 27 | 36.8/6.0 | 33.8/6.5 | |
| 55 | Q42546 | At5g63980 | – | – | –2.1 | – | – | SAL1 phosphatase | 818/35/15 | 46 | 37.8/5.0 | 40.4/5.3 | |
| Unknown | |||||||||||||
| 56 | Q8L768 | At1g78150 | –2.2 | – | – | –2.3 | – | Uncharacterized protein | 773/16/13 | 46 | 29.7/6.2 | 30.1/6.6 | |
| 57 | Q94EG6 | At5g02240 | – | – | 2.3 | – | – | Uncharacterized protein | 277/8/5 | 20 | 41.9/6.0 | 20.1/5.5 | |
| 58 | Q94EG6 | At5g02240 | – | 2.4 | – | – | – | Uncharacterized protein | 873/27/14 | 60 | 27.1/6.2 | 27.3/6.4 | |
| 59 | Q9LJE5 | At3g13460 | – | –3.6 | – | – | – | Uncharacterized protein | 500/8/8 | 16 | 72.7/5.7 | 93.0/6.1 | |
| 60 | Q9SZP8 | At4g38710 | – | – | 3.9 | – | – | Glycine-rich protein | 519/10/8 | 25 | 49.0/5.1 | 63.0/5.4 | |
| 61 | Q941B7 | At2g39730 | – | – | 2.1 | 2.3 | 3.3 | At2g39730/T5I7.3 | 804/29/13 | 52.4/5.7 | 47.8/5.1 | ||
| 62 | Q94K71 | At3g48415 | – | – | – | 20.8 | – | Haloacid dehalogenase-like hydrolase domain-containing | 805/22/15 | 45 | 34.7/8.3 | 27.6/5.4 | |
| no ID | |||||||||||||
| 63 | – | – | – | 3.1 | – | No ID | |||||||