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. 2010 Jan;152(1):4–18. doi: 10.1104/pp.109.150425

Table I.

Proteins preferentially accumulated in cortical parenchyma compared with stele tissue of maize primary roots identified after 2-DE separation and nano-HPLC-ESI-MS/MS analysis of trypsin-digested proteins matched against the NCBI.nr protein database entries

Preferentially accumulated proteins, ≥2-fold change; t test, P < 0.01 in three independent biological replicates.

Spot No. Cortex Specificitya MOWSE Scoreb Sequence Coveragec Mr Predicted/Mr Geld pI Predicted/pI Gele Function NCBI.nr [Species] Accession No.f t Test Pg FDR Ph
Metabolism
1 Cortex only 231 12 41.6/44.1 5.3/5.4 12-Oxo-phytodienoic acid reductase [Zea mays] AAY26523 <0.001 0.007
2 Cortex only 259 16 41.6/43.6 5.3/5.6 12-Oxo-phytodienoic acid reductase [Z. mays] AAY26523 <0.001 0.048
3 Cortex only 697 19 64.2/65.3 6.2/5.5 β-d-Glucoside glucohydrolase [Z. mays] P49235 0.001 0.014
4 Cortex only 934 23 82.0/84.9 5.6/5.5 Hydroxymethylbutenyl 4-diphosphate synthase [Z. mays] AAT70081 <0.001 0.010
5 Cortex only 246 3 113.1/79.2 5.9/6.0 Glycosyl hydrolase [Oryza sativa] ABG22500 <0.001 0.006
6 Cortex only 319 9 71.8/70.1 7.2/6.2 Oxidoreductase [Z. mays] CAA12157 <0.001 0.003
7 Cortex only 212 6 66.5/70.4 5.8/6.1 Asparagine synthetase [Z. mays] P49094 <0.001 0.003
8 Cortex only 140 11 29.3/25.8 6.8/6.3 Haloacid dehalogenase-like hydrolase [O. sativa] NP_001058303i 0.003 0.023
9 Cortex only 204 9 44.0/41.7 6.0/6.4 Glutamate dehydrogenase [Z. mays] AAB51595 0.003 0.022
10 Cortex only 169 8 43.5/35.2 6.1/5.4 Cysteine synthase 1 [O. sativa] EAZ15034i <0.001 0.002
11 Cortex only 280 8 102.4/110.5 5.7/5.4 Pyruvate, orthophosphate dikinase [Z. mays] AAA33498 0.006 0.035
12 Cortex only 334 13 64.2/66.0 6.2/5.6 β-d-Glucoside glucohydrolase [Z. mays] P49235 0.004 0.027
13 Cortex only 125 5 77.5/90.5 5.7/5.5 Acetyl-CoA synthetase [O. sativa] NP_001046995i <0.001 0.004
14 Cortex only 242 8 51.6/51.2 5.5/6.0 UDP-Glc pyrophosphorylase [O. sativa] NP_001045689i <0.001 0.002
15 Cortex only 542 18 63.1/57.3 8.6/6.2 ζ-Carotene desaturase [Z. mays] Q9ZTP4 0.005 0.032
16 Cortex only 278 15 41.2/44.5 5.9/6.0 Cysteine desulfurase [O. sativa] ABA97759 <0.001 0.002
17 Cortex only 297 9 60.8/70.3 6.0/6.2 Aspartyl-tRNA synthetase [O. sativa] NP_001047770i 0.001 0.013
18 Cortex only 586 23 34.5/34.6 6.2/6.4 Aldose reductase [Z. mays] ABF61890 <0.001 0.011
19 Cortex only 386 20 39.4/33.8 7.7/6.4 Pyridoxine biosynthesis protein [O. sativa] EAZ02455 <0.001 0.006
20 Cortex only 277 15 41.7/48.3 5.9/6.2 12-Oxo-phytodienoic acid reductase [Z. mays] AAY26521 0.006 0.035
21 Cortex only 233 12 47.5/40.6 7.6/6.5 Aspartate aminotransferase [O. sativa] BAA23815 <0.001 0.006
22 Cortex only 258 15 40.1/35.0 8.4/6.0 Aspartate/glutamate/uridylate kinase [O. sativa] EAY75934i <0.001 0.002
23 22.9 1237 34 64.2/63.7 6.2/5.8 β-d-Glucoside glucohydrolase [Z. mays] P49235 <0.001 0.002
24 18.2 890 19 64.2/64.5 6.2/5.7 β-d-Glucoside glucohydrolase [Z. mays] P49235 <0.001 0.002
25 14.5 181 5 64.2/60.0 6.2/5.6 β-d-Glucoside glucohydrolase [Z. mays] P49235 <0.001 0.002
26 8.7 730 32 39.2/37.9 5.6/5.6 Glutamine synthetase [Z. mays] BAA03433 <0.001 0.006
27 8.7 256 14 39.2/37.8 5.6/5.8 Glutamine synthetase [Z. mays] BAA03433 0.002 0.018
28 8.0 190 7 64.2/61.5 6.2/5.5 β-d-Glucoside glucohydrolase [Z. mays] P49235 <0.001 0.006
29 7.1 340 5 113.9/130.0 5.9/6.3 Glycosyl hydrolase [O. sativa] ABG22500 0.003 0.028
30 6.5 135 5 49.6/42.6 6.6/6.4 Alanine-glyoxylate aminotransferase [O. sativa] EAY89931i <0.001 0.003
31 5.0 244 9 64.2/35.8 6.2/5.8 β-d-Glucoside glucohydrolase [Z. mays] P49235 0.005 0.032
32 4.1 518 12 64.5/71.3 6.5/6.0 Phosphoglycerate dehydrogenase [O. sativa] BAD09434 0.003 0.026
33 3.9 149 7 44.5/44.8 6.4/6.1 Glutamate dehydrogenase A [O. sativa] EAY86911i <0.001 0.010
34 3.3 581 20 64.2/59.9 6.2/5.7 β-d-Glucoside glucohydrolase [Z. mays] P49235 0.002 0.017
35 3.2 1104 22 102.4/108.4 5.7/5.4 Pyruvate, orthophosphate dikinase [Z. mays] AAA33498 0.001 0.013
36 3.0 390 8 77.5/88.7 5.7/5.6 Acetyl-CoA synthetase [O. sativa] NP_001046995i 0.004 0.029
37 2.8 411 18 42.1/42.5 5.6/5.6 3-Phosphoglycerate kinase [Z. mays] P12783 0.001 0.013
38 2.5 266 11 54.8/57.2 5.6/5.6 Aldehyde dehydrogenase RF2D [Z. mays] AAL99611 0.006 0.036
39 2.5 303 7 76.3/61.5 5.7/5.6 Ketol-acid reductoisomerase [O. sativa] EAY75202i <0.001 0.005
40 2.2 132 8 44.0/43.3 6.1/6.1 Glutamate dehydrogenase [Z. mays] Q43260 0.003 0.023
41 2.1 597 22 44.0/41.8 6.1/6.3 Glutamate dehydrogenase [Z. mays] Q43260 0.003 0.023
42 2.1 306 15 32.4/25.8 7.0/5.0 Triosephosphate isomerase [O. sativa] NP_001063777 0.002 0.017
43 2.1 737 27 52.5/47.8 5.8/5.9 Glutathione synthetase [Z. mays] CAE18179 0.009 0.047
Signal transduction
44 Cortex only 127 3 69.8/85.3 5.9/5.7 Metallophosphatase [O. sativa] NP_001062330i <0.001 0.002
Protein fate
45 Cortex only 524 11 105.6/115.8 5.5/5.4 Lon protease homolog 2 [Z. mays] NP_001105895 0.002 0.018
46 Cortex only 278 20 32.6/41.4 4.6/5.5 Histone deacetylase 2b [Z. mays] Q9M4U5 0.007 0.041
Protein synthesis
47 Cortex only 589 29 46.5/50.4 5.4/5.4 Translational initiation factor eIF-4A [Z. mays] NP_001105372 <0.001 0.011
Disease/defense/stress response
48 Cortex only 1308 23 102.0/100.0 6.6/5.6 ATP-dependent Clp protease [O. sativa] NP_001066442 0.001 0.012
49 3.5 198 22 25.8/26.1 5.4/5.4 Glutathione S-transferase GST 26 [Z. mays] AAG34834 0.008 0.041
50 2.3 433 16 50.2/45.5 5.2/5.1 UDP-Glucosyltransferase BX9 [Z. mays] AAL57038 0.006 0.035
51 2.3 237 19 26.7/26.4 6.1/6.3 Aluminum-induced protein-like protein [Setaria italica] ABM97609 <0.001 0.012
Energy
52 Cortex only 511 17 61.9/75.5 5.9/5.4 Vacuolar ATP synthase catalytic subunit A [Z. mays] P49087 <0.001 0.002
53 2.4 834 25 61.9/74.1 5.9/5.5 Vacuolar ATP synthase catalytic subunit A [Z. mays] P49087 0.004 0.030
Cell fate
54 Cortex only 291 10 61.1/46.1 6.9/5.4 Actin-interacting protein [O. sativa] BAC79943 0.001 0.013
Unknown function
55 Cortex only 151 14 22.5/20.8 7.8/6.5 Unknown protein [O. sativa] NP_001042770i <0.001 0.003
56 Cortex only 163 14 22.5/20.3 7.8/6.5 Unknown protein [O. sativa] NP_001042770i <0.001 0.012
57 Cortex only 171 4 66.2/117.0 4.6/4.7 Unknown protein [O. sativa] EAY76673i <0.001 0.002
58 Cortex only 180 6 52.1/54.8 5.2/5.6 Unknown protein [O. sativa] AAM93677i 0.005 0.032
59
 2.7
 215
 9
 40.2/37.4
 5.7/5.9
 Herbicide safener-binding protein [Z. mays] AAC12715
 0.009
 0.048
a

Ratio of accumulation (fold change) of a particular protein between primary root cortex versus stele tissue.

b

Probability-based MOWSE score is defined as –10 × log(P), where P is the probability that the observed match is a random event. Scores > 43 indicate identity or extensive homology (P < 0.05). Protein scores are derived from ion scores as a nonprobabilistic basis for ranking protein hits.

c

Percentage of predicted protein sequence covered by matched peptides.

d

Theoretical molecular mass of predicted protein/experimental molecular mass of protein on the gel.

e

Theoretical pI of predicted protein/experimental pI of protein on the gel.

f

Function of sequenced peptides obtained via automated algorithm of the MASCOT software (www.matrixscience.com) from the NCBI.nr database.

g

P values obtained via Student's t test after comparing protein accumulation of three biological replicates of primary root cortex versus stele tissue (cutoff, P ≤ 0.01).

h

P values of the linear contrasts were adjusted according to Wald tests (cutoff, P ≤ 0.05).

i

For protein accessions identified by MASCOT that had no functional annotation, a function was assigned via BLASTP searches of the corresponding protein accession numbers (cutoff, E ≤ 1e−10).