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Table 2 Functional classification of up-regulated proteins

From: Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ and a novel comparison system based on a notched-belly mutant with white-belly

Accession

Protein Name

Score

Mass (kDa)

Cov. (%)

Unique peptide

C2/C1

T2/T1

C/T

Amino acid metabolism

       

gi|385717668

5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase

768

100.7

12.1

7

0.322

0.260

1.238

gi|77548611

2-isopropylmalate synthase A

677

78.0

23

9

0.938

0.721

1.301

Carbohydrate metabolism

       

gi|78099751

Fructose-bisphosphate aldolase cytoplasmic isozyme

921

48.7

24

4

0.855

0.662

1.292

gi|113632010

Triosephosphate isomerase, chloroplastic

315

38.8

20.4

4

0.400

0.290

1.379

gi|113548195

Probable rhamnose biosynthetic enzyme 1

241

91.2

7.3

3

0.382

0.261

1.464

gi|40253646

putative starch synthase DULL1

155

231.2

3

5

1.451

0.990

1.466

gi|113580063

UDP-glucose 4-epimerase GEPI48

183

45.8

6.8

2

0.312

0.208

1.500

gi|113548194

UDP-glucuronic acid decarboxylase 1

220

46.1

14.6

3

0.566

0.340

1.665

gi|222628767

2-oxoglutarate dehydrogenase, mitochondrial

249

129.0

4.9

4

0.163

0.096

1.698

gi|113549799

UDP-glucose 6-dehydrogenase

188

65.0

11.9

3

0.173

0.081

2.136

gi|75327567

Probable cinnamyl alcohol dehydrogenase 6

92

46.0

4.2

1

0.437

0.135

3.237

gi|75133690

UDP-arabinopyranose mutase 3

243

49.9

16.7

5

0.270

0.074

3.649

gi|75156168

Hexokinase-1

152

56.2

4.6

2

0.333

0.054

6.167

Cell defense

        

gi|113533098

Heterogeneous nuclear ribonucleoprotein A2/B1-like

131

50.1

10.5

2

1.567

1.241

1.263

gi|113580000

Late embryogenesis abundant protein Lea14-A

63

20.4

7.3

1

1.528

1.128

1.355

gi|22711545

Putative cytochrome P450

58

120.8

0.9

1

0.088

0.051

1.725

gi|113649843

P21 protein, putative, expressed

269

29.3

21.8

5

1.632

0.824

1.981

gi|113649501

Pathogenesis-related protein 1

197

21.3

38.1

4

1.380

0.500

2.760

gi|113649505

Major pollen allergen Bet v 1-D/H

1402

21.5

75.3

10

1.814

0.567

3.199

Coenzyme metabolism

       

gi|54291831

C-1-tetrahydrofolate synthase, cytoplasmic

57

36.7

4.8

1

0.407

0.159

2.560

Energy production

       

gi|113548489

ATP-dependent transporter ycf16, putative, expressed

172

38.0

15.1

3

0.900

0.747

1.205

gi|75294330

Probable succinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial

205

41.3

12.1

3

0.998

0.645

1.547

gi|113535585

Putative vacuolar proton-ATPase

475

79.8

14

2

0.400

0.110

3.636

gi|113533574

Putative vacuolar ATPase B subunit

1023

60.4

30.9

9

0.304

0.082

3.707

Lipid metabolism

        

gi|113595159

Sterol carrier protein 2-like

210

18.4

28.7

3

1.084

0.820

1.322

gi|122248693

Non-specific lipid-transfer protein 3

241

14.1

24.8

2

1.598

1.122

1.424

Protein synthesis, folding and degradation

       

gi|113579500

Protein translation factor SUI1 homolog

63

16.8

11.3

1

0.977

0.797

1.226

gi|122246932

Cysteine proteinase inhibitor 8

216

13.5

36.6

2

1.247

0.995

1.253

gi|38605801

40S ribosomal protein S27

288

7.4

66.7

2

0.855

0.672

1.272

gi|125584147

Tubulin-specific chaperone A

67

17.2

8

1

1.801

1.404

1.283

gi|108711183

26S proteasome non-ATPase regulatory subunit 10, putative, expressed

259

29.4

25.4

4

0.936

0.719

1.302

gi|113535779

26S proteasome regulatory particle triple-A ATPase subunit 6

177

58.0

18.6

5

0.437

0.326

1.340

gi|1703380

ADP-ribosylation factor 2

336

24.4

35.4

5

0.623

0.463

1.346

gi|222641792

Heat shock protein 81-2

461

56.5

19.5

2

1.535

1.110

1.383

gi|113531460

Bowman-Birk type wound-induced proteinase inhibitor WIP1

167

15.2

10

1

1.353

0.946

1.430

gi|113649350

Eukaryotic translation initiation factor 5A-2

212

22.6

29.4

3

1.179

0.821

1.436

gi|730456

40S ribosomal protein S19

375

20.1

41.1

6

0.860

0.581

1.480

gi|391875

40S ribosomal protein S20

135

17.7

21.4

1

0.847

0.562

1.507

gi|113550094

T-complex protein 1 subunit theta

244

70.8

11.7

4

0.367

0.240

1.529

gi|14589381

Alanine--tRNA ligase

228

95.3

9.9

5

0.797

0.474

1.681

gi|122232855

Clathrin heavy chain 1

229

224.0

6

7

0.490

0.274

1.788

gi|62900360

Importin subunit alpha-1a

159

67.0

5.3

2

0.290

0.156

1.859

gi|255672966

Putative density regulated protein drp1

244

28.6

38.2

4

1.035

0.547

1.892

gi|122169274

Coatomer subunit delta-2

93

69.0

7.3

3

0.521

0.220

2.368

gi|113548306

40S ribosomal protein S7

90

28.9

16.1

2

0.450

0.173

2.601

gi|75325389

Eukaryotic initiation factor 4A-3

428

53.5

25.1

8

0.514

0.173

2.971

gi|38347158

Chaperone protein ClpC1, chloroplastic

294

116.5

12.5

6

0.986

0.295

3.342

Redox homeostasis

       

gi|122166938

Peroxidase 2

172

35.5

13.1

3

1.418

1.045

1.357

Secondary metabolites biosynthesis

       

gi|75261413

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, chloroplastic

180

93.3

6

3

0.167

0.027

6.185

Signal transduction

       

gi|122235035

Calmodulin-3

276

20.2

22.8

1

1.310

1.083

1.210

gi|75323484

Calmodulin-2

510

20.5

22.8

1

1.434

1.180

1.215

gi|113532001

Ras-related protein Rab7

136

28.0

16.9

3

0.692

0.390

1.774

Transcription

        

gi|113622935

Putative quinone-oxidoreductase QR2

199

26.1

25.1

4

0.625

0.478

1.308

Transport

        

gi|113639089

Protein CutA1, chloroplastic

348

21.6

22.9

3

1.327

1.045

1.270

gi|113649744

Sulfurtransferase

461

47.3

32.8

8

0.977

0.680

1.437

gi|113578690

ADP, ATP carrier protein 1, mitochondrial

197

50.6

9.2

3

0.502

0.137

3.664

Unknown pathway

       

gi|113549649

hypothetical protein

166

12.0

17.4

2

1.777

1.423

1.249

gi|113579243

Pleckstrin homology domain-containing protein 1

129

21.9

7

1

0.916

0.728

1.258

gi|113596594

Os06g0711900

105

17.7

11.2

1

1.618

1.267

1.277

gi|3492928

16 kDa oleosin isoform R16

131

17.7

6.1

1

1.363

1.031

1.322

gi|113623942

Os08g0459300

204

27.3

29.2

3

1.222

0.920

1.328

gi|113596416

Putative phytocyanin protein, PUP2

158

28.4

12.2

3

1.217

0.908

1.340

gi|113532536

Outer-envelope membrane of Chloroplasts 34-like

425

747.7

2.5

10

1.210

0.871

1.389

gi|77550956

EF hand family protein

164

12.1

10.4

1

1.423

1.021

1.394

gi|75106519

Early nodulin-like protein 1

512

26.8

12.7

2

1.577

1.096

1.439

gi|53792234

Bowman-Birk type bran trypsin inhibitor

77

33.2

4.5

1

1.109

0.752

1.475

gi|46981317

unknown protein

70

60.7

4.5

2

0.636

0.380

1.674

gi|113547324

Gamma-thionin PPT, putative, expressed

573

10.7

27.2

2

1.552

0.920

1.687

gi|113623527

Os08g0327700 (Putative seed maturation protein)

224

17.6

13.3

1

1.792

0.965

1.857

gi|113578614

Putative pentatricopeptide repeat-containing protein At1g10330

51

58.4

1.4

1

1.884

0.516

3.651

  1. Note: Notched-belly grain without white-belly was used as the control. The effect of embryo was quantified by comparison between the bottom part (T2) and upper part (T1). Comparison of the bottom part (C2) and upper part (C1) of grain with white-belly indicated the compound effect of embryo and chalkiness. Therefore, the effect of chalkiness can be evaluated through a further comparison between C2 vs C1 and T2 vs T1, by which the embryo effect was eliminated. Cov. , average percentage of assigned peptides to the predicted protein.
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BMC Plant Biology

ISSN: 1471-2229

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