Table I MALDI-TOF MS identification of proteins preferentially accumulated in wild-type or in fl mutant cotton ovules
Spot no.aProtein nameNCBI Accession no.pI/exp.b molecular mass (kDa)pI/theo.c molecular mass (kDa)Score/cov.d (%)Matched/searchedeRelative protein contentRatio WT/FL
WT-10FL-10
1ProfilinABO437175.33/13.015.38/14.4172/5610/600.397 ± 0.0340.205 ± 0.0261.94
2fMajor latex-like proteinFJ4152025.44/14.835.46/17.1686/6010/860.236 ± 0.0280.121 ± 0.0141.95
3Annexin 1AAR132886.31/15.816.19/36.15172/5520/640.103 ± 0.0170.017 ± 0.0096.06
6AnnexinAAB679936.08/16.106.41/36.0399/3513/680.037 ± 0.0050g
18fAnnexinFJ4151736.52/28.496.74/35.98123/3814/600.065 ± 0.0210.022 ± 0.0082.95
5Fiber annexinAAC333056.11/16.046.34/36.2199/3715/810.075 ± 0.0150.038 ± 0.0111.97
4fCopper,zinc-superoxide dismutaseFJ4152035.83/15.985.47/15.36106/9210/590.162 ± 0.0210.084 ± 0.0251.93
7fCopper,zinc-superoxide dismutaseFJ4152035.83/16.355.47/15.3688/9210/93
8fPeroxiredoxinFJ4151745.35/17.415.58/17.30140/7410/440.127 ± 0.0280.048 ± 0.0082.65
9fDimethylmenaquinone methyltransferaseFJ4151795.41/18.545.60/18.05104/507/420.145 ± 0.0230.080 ± 0.0081.81
10Benzoquinone reductaseABN123216.09/21.656.09/21.6569/395/490.295 ± 0.0130.053 ± 0.0075.57
13Benzoquinone reductaseABN123216.27/27.606.09/21.6580/395/56
14Benzoquinone reductaseABN123206.47/27.836.20/21.7982/315/290.348 ± 0.0390.034 ± 0.01210.24
88fBenzoquinone reductaseFJ4151837.68/24.726.97/21.7494/4812/530.131 ± 0.0190g
11Ascorbate peroxidaseABR186075.13/27.495.93/27.7484/529/50
12Ascorbate peroxidaseABR186075.43/27.515.93/27.7479/447/100
15Ascorbate peroxidaseABR186075.68/27.845.93/27.7490/466/77
16Ascorbate peroxidaseABR186075.29/27.875.93/27.7478/479/590.239 ± 0.0250.040 ± 0.0175.98
19Ascorbate peroxidaseABR186075.32/28.705.93/27.74101/499/51
20Ascorbate peroxidaseABR186075.64/28.755.93/27.74151/6415/41
21Ascorbate peroxidaseABR186075.15/29.285.62/27.58112/6013/67
17fAscorbate peroxidaseFJ4151854.96/27.895.62/27.5866/385/600.207 ± 0.0320.043 ± 0.0154.81
38fStromal ascorbate peroxidaseFJ4151866.24/36.788.89/41.0585/3513/750.102 ± 0.0140.047 ± 0.0152.17
40fStromal ascorbate peroxidaseFJ4151866.10/37.048.89/41.0573/289/100
22fα-1,4-glucan phosphorylaseFJ4152114.94/30.215.32/10.67108/2319/940.132 ± 0.0100g
23fS-Formylglutathione hydrolaseFJ4151886.59/30.656.82/32.1877/4710/890.120 ± 0.0360.050 ± 0.0022.40
24fTriose-phosphate isomeraseFJ4151776.53/31.546.00/27.47142/8215/1100.253 ± 0.0350.170 ± 0.0191.49
25f20 S proteasome subunit α-1FJ4151816.44/31.805.91/27.39112/4711/490.105 ± 0.0090.035 ± 0.013.00
26fHeat shock protein 70FJ4151966.27/32.835.07/71.5774/199/770.146 ± 0.0100.036 ± 0.0254.06
68fHeat shock protein 70FJ4151964.75/52.955.10/71.3784/2615/99
63fHeat shock protein 70FJ4151994.59/49.925.10/71.3588/279/950.113 ± 0.0070.043 ± 0.0412.63
67fHeat shock protein 70FJ4151944.69/52.905.14/71.2889/219/370.468 ± 0.0270.134 ± 0.0303.49
90fHeat shock protein 70FJ4151947.52/33.125.14/71.2884/209/65
73fHeat shock protein 70FJ4151954.75/54.075.07/71.5790/138/470.059 ± 0.0070.010 ± 0.0115.90
27fCatalaseFJ4151876.30/33.596.68/57.2573/3016/840.197 ± 0.0320.091 ± 0.0152.16
28fSerine hydroxymethyltransferaseFJ4151805.54/34.187.57/52.3895/269/590.091 ± 0.0080.014 ± 0.0016.50
31fSerine hydroxymethyltransferaseFJ4151805.83/34.827.57/52.3875/3612/76
29fLactoylglutathione lyaseFJ4152045.71/34.385.69/32.6169/3411/690.202 ± 0.0160g
30fα-Soluble NSFh attachment proteinFJ4151715.08/34.755.11/33.05120/399/230.110 ± 0.0330.034 ± 0.0123.24
32fUER1FJ4151675.94/34.945.73/33.95180/6218/790.253 ± 0.0300.253 ± 0.0301.78
33fUER1FJ4151676.22/34.975.73/33.95215/6415/31
34fFructokinaseFJ4151695.05/36.085.28/35.20206/5816/410.080 ± 0.0020.045 ± 0.0091.78
35EnolaseABW216885.21/36.285.49/47.9885/297/780.049 ± 0.0030g
36ActinAAP734545.43/36.645.23/41.9090/4612/630.178 ± 0.0270.027 ± 0.0286.59
52ActinAAP734525.62/42.355.44/41.9469/297/860.264 ± 0.0170.018 ± 0.02014.67
53ActinAAP734575.56/43.295.31/41.91149/6028/1420.244 ± 0.030.039 ± 0.0366.26
71ActinAAP734605.45/53.585.37/41.94163/5722/910.189 ± 0.0230.120 ± 0.0321.58
37fGranule-bound starch synthaseFJ4151894.97/36.648.79/63.8480/208/550.087 ± 0.0120g
39fGranule-bound starch synthaseFJ4152054.91/36.788.59/67.73135/3513/890.090 ± 0.0160.019 ± 0.0114.76
41fGlutamine synthaseFJ4151785.64/37.125.77/39.36140/4310/500.078 ± 0.0060g
42fMalate dehydrogenaseFJ4151926.14/38.506.10/36.4593/2710/770.337 ± 0.0040.222 ± 0.0281.52
56fMalate dehydrogenaseFJ4151926.67/46.156.10/35.8788/438/100
43Phenylcoumaran benzylic ether reductase-like proteinABN123225.58/38.895.76/33.8992/3511/480.227 ± 0.0210.102 ± 0.0222.23
51Phenylcoumaran benzylic ether reductase-like proteinABN123225.87/41.465.76/33.89129/5818/97
45β-Tubulin 19ABY866655.75/39.764.76/50.65173/5826/700.073 ± 0.0340g
46α-Tubulin 4AAN330005.57/39.905.36/34.41207/6419/400.145 ± 0.0070.059 ± 0.0182.46
49α-Tubulin 4AAN330005.43/40.905.36/34.41107/4412/65
48α-TubulinABO477385.72/40.454.97/50.29159/4319/380.155 ± 0.0290g
50fGlyceraldehyde-3-phosphate dehydrogenase C subunitFJ4152066.61/41.247.70/36.6573/337/870.234 ± 0.0300.115 ± 0.0522.04
54f2-Nitropropane dioxygenaseFJ4151765.43/43.735.32/36.17211/6818/620.330 ± 0.0090.134 ± 0.0332.46
55fQuinone oxidoreductaseFJ4151755.21/45.905.28/34.39149/6716/1060.088 ± 0.0140g
57Gibberellin 20-oxidase 1ABA014825.23/48.015.35/41.72215/6424/840.030 ± 0.0070g
58Flavanone 3-hydroxylaseABM647995.33/48.105.43/41.75171/6626/1300.485 ± 0.0070.226 ± 0.0232.14
59fMannitol dehydrogenaseFJ4151915.93/49.115.85/39.57100/6116/900.252 ± 0.0320.144 ± 0.0261.75
60fAdenosine kinaseFJ4151705.46/49.665.47/37.81200/5915/380.059 ± 0.0180.145 ± 0.0281.40
61fAdenosine kinaseFJ4151705.31/49.665.47/37.81128/5518/64g
62fPhosphoglycerate dehydrogenaseFJ4151905.20/49.847.14/64.0681/237/540.111 ± 0.0090g
65fPhosphoglycerate dehydrogenaseFJ4151905.13/50.357.14/64.0677/278/100
64fPyruvate dehydrogenase α subunitFJ4151976.74/50.177.16/43.6979/309/1000.222 ± 0.0130.157 ± 0.0081.41
66Anthocyanidin reductaseABM648025.53/51.745.54/36.54138/4916/860.358 ± 0.0030g
69fLuminal binding proteinFJ4152004.57/53.095.13/73.5781/3117/950.062 ± 0.0160.015 ± 0.0124.13
70fLuminal binding proteinFJ4152004.50/53.555.13/73.5776/239/100
72fLuminal binding proteinFJ4152004.55/53.945.13/73.57104/2510/67
74fPhosphoglycerate kinaseFJ4151726.14/56.405.97/42.29140/4414/590.063 ± 0.0080.035 ± 0.0031.80
75Chloroplast biotin carboxylaseABP988136.30/57.927.57/59.1794/3419/850.083 ± 0.0110.049 ± 0.0101.69
77Chloroplast biotin carboxylaseABP988136.31/59.647.57/59.17139/6126/101
76fDihydrolipoamide dehydrogenaseFJ4151936.62/59.376.93/54.1370/258/1000.118 ± 0.0260g
78fUGP2FJ4151655.54/60.415.62/51.45155/4918/1000.205 ± 0.0150.145 ± 0.0231.42
79fUGP1FJ4151646.07/61.705.81/51.74132/5217/610.178 ± 0.0160.092 ± 0.0141.93
80fUGP1FJ4151646.10/61.705.81/51.74216/6122/63
81fUGD1FJ4151666.11/62.845.84/53.64183/5923/1090.124 ± 0.0160.057 ± 0.0132.18
83fUGD1FJ4151666.30/64.125.84/53.64188/5318/49
82fmyo-Inositol-1-phosphate synthaseFJ4151685.69/63.535.46/56.54207/5424/1060.090 ± 0.0060.046 ± 0.0101.96
84Acyltransferase-like proteinAAL679945.67/64.475.67/48.29107/4022/1080.100 ± 0.0130.019 ± 0.0085.26
85Acyltransferase-like proteinAAL679945.56/64.825.67/48.2972/3815/110
86fPyruvate decarboxylaseFJ4152016.57/69.526.13/60.7799/3011/1000.128 ± 0.0330.025 ± 0.0145.00
87fGlycine-rich RNA-binding proteinFJ4151847.82/15.017.82/17.08111/6213/720.116 ± 0.0300g
89Manganese-superoxide dismutaseAAC784697.49/25.408.54/22.14158/7516/1000.089 ± 0.0150.041 ± 0.0082.17
91fGlyceraldehyde-3-phosphate dehydrogenaseFJ4151827.74/43.727.06/37.0492/5815/1000.167 ± 0.0230.048 ± 0.0153.48
92fIsocitrate dehydrogenaseFJ4151987.32/53.156.29/46.41188/6328/1000.381 ± 0.0300.256 ± 0.0291.49
93fIsocitrate dehydrogenaseFJ4151987.07/53.296.29/46.41140/5723/100
94fEukaryotic translation initiation factor 5AGU2950625.55/18.885.61/17.6396/529/610.156 ± 0.0260.293 ± 0.0240.53
95fChalcone isomeraseGU2950634.84/29.854.85/23.4295/6710/660.104 ± 0.0210.177 ± 0.0170.59
96fTriose-phosphate isomeraseGU2950645.52/30.186.66/33.50101/5316/1380.051 ± 0.0090.122 ± 0.0160.42
97fThiazole biosynthetic enzymeGU2950685.03/36.815.64/38.24170/6317/490.048 ± 0.0080.155 ± 0.0240.31
98fTransaldolaseGU2950654.91/45.565.78/43.06129/3310/180.036 ± 0.0050.089 ± 0.0120.40
100fTransaldolaseGU2950655.09/46.625.78/43.06123/2912/32
99fU2 small nuclear ribonucleoprotein AGU2950665.06/45.904.97/32.19204/6818/500.062 ± 0.0030.237 ± 0.0330.26
101Chalcone synthaseABS525736.11/54.176.12/42.9887/3511/450.039 ± 0.0100.104 ± 0.0260.38
102Protein-disulfide isomeraseABO418435.01/65.305.07/55.89203/5924/770.051 ± 0.0100.102 ± 0.0030.50
103fRNA helicase-like proteinGU2950675.91/69.245.65/56.15201/4317/320.062 ± 0.0120.121 ± 0.0200.51
104Betaine-aldehyde dehydrogenaseAAR238165.44/69.435.60/55.37100/4219/1030.055 ± 0.0110.114 ± 0.0120.48
  • a Protein spots are arranged from lowest to highest molecular mass with spots encoded by the same cotton cDNA quantified as one protein and spots presumably encoded by the same gene family located next to each other. Spots 1–93 were preferentially accumulated in the wild type, and spots 94–104 were preferentially accumulated in the mutant.

  • b Experimental.

  • c Theoretical.

  • d Coverage.

  • e Number of matched/searched polypeptides.

  • f Sixty-eight polypeptides encoded by 50 putative full length and one partial (spot 22, FJ415211) cotton cDNAs obtained for the first time in the current work.

  • g Protein spots only observed in WT-10.

  • h N-Ethylmaleimide-sensitive factor.