Table II. Proteomic analysis of rice coleoptiles in response to anoxia or switch from air to anoxia.
Proteins selected from DIGE corresponding to Figure 1, A and B, and iTRAQ (Supplemental Table S2) were identified by MS/MS (Protein ID) with corresponding rice gene numbers (Os Gene No.). Details of the matched protein size, number of peptides identified, and percentage coverage are shown in Supplemental Table S1. Transcript abundance differences between anoxic (4 d) and aerated (4 d) rice coleoptiles derived from independent microarray data (Lasanthi-Kudahettige et al., 2007) have been incorporated (significant increase [positive, boldface], significant decrease [negative, boldface italic]). Protein spots chosen for MS/MS analysis met the following criteria in at least one analysis: a protein abundance difference of 1.5 or greater where proteins were higher in anoxic samples (positive, boldface) and those higher in aeration (negative, boldface italic), P < 0.05, and an abundance high enough on preparative gels for subsequent MS identification. FAD, Fold abundance difference; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; iPGAM, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; MetSyn, cobalamin-independent Met synthase; N/S, not significant; 3-PGDH, d-3-phosphoglycerate dehydrogenase; PSAT, phospho-Ser aminotransferase; S, significant; SHMT, Ser hydroxymethyltransferase; Sig., significantly different from 1 or not; TGM, transformed geometric mean; X, no data.
| Functional Category | Os Gene No. | Protein ID | DIGE: 3-10NL |
DIGE: 3-11NL |
DIGE: 3-10NL |
iTRAQ |
Array | |||||||
| 6 d N2/4 d Air |
6 d N2/4 d Air |
4 d Air 1 d N2/4 d Air |
6 d N2/4 d Air |
4 d N2/4 d Air | ||||||||||
| Spot | FAD | P | Spot | FAD | P | Spot | FAD | P | TGM | Sig. | FAD | |||
| Sugar metabolism, | Os03g28330.1 | Suc synthase | – | X | X | – | X | X | – | X | X | 1.6 | S | 2 |
| glycolysis, | Os06g09450.1 | Suc synthase | – | X | X | – | X | X | – | X | X | 1.7 | S | 2 |
| fermentation, | Os01g60190.1 | iPGAM | 31 | 3.3 | 4.E-04 | 20 | 5.7 | 5.E-04 | 27 | 1.3 | 1.E-01 | −1.0 | N/S | 2 |
| and TCA cycle | Os01g60190.1 | iPGAM | 32 | 4.3 | 4.E-06 | 21 | 6.1 | 3.E-05 | 26 | 1.5 | 9.E-03 | −1.0 | N/S | 2 |
| Os10g08550.1 | Enolase | 33 | 7.5 | 5.E-09 | 18 | 5.7 | 9.E-04 | 28 | 2.4 | 7.E-04 | 1.2 | S | 2 | |
| Os10g08550.1 | Enolase | 34 | 2.2 | 3.E-05 | 19 | 2.8 | 2.E-03 | 29 | 1.5 | 8.E-04 | 1.2 | S | 2 | |
| Os08g02120.1 | Fructokinase-2 | – | X | X | – | X | X | – | X | X | −2.2 | S | −2 | |
| Os05g33380.1 | Aldolase | 16 | 4.7 | 5.E-06 | – | X | X | 5 | 2.1 | 3.E-04 | 2.0 | S | N/S | |
| Os01g67860.1 | Aldolase | – | X | X | – | X | X | – | X | X | 2.2 | S | N/S | |
| Os10g08022.1 | Aldolase | – | X | X | – | X | X | – | X | X | 2.3 | S | X | |
| Os04g40950.1 | GAPDH | 6 | 2.2 | 7.E-04 | 6 | 2.4 | 2.E-03 | 4 | 1.1 | 8.E-02 | 1.4 | S | N/S | |
| Os04g40950.1 | GAPDH | 10 | 3.6 | 7.E-05 | – | X | X | 11 | 1.0 | 7.E-01 | 1.4 | S | N/S | |
| Os04g40950.1 | GAPDH | – | X | X | 8 | 2.6 | 1.E-03 | – | X | X | 1.4 | S | N/S | |
| Os02g38920.1 | GAPDH | 18 | 13.2 | 5.E-06 | – | X | X | 9 | 1.7 | 2.E-03 | 1.8 | S | 3 | |
| Os02g38920.1 | GAPDH | 17 | 6.7 | 4.E-08 | – | X | X | 8 | 1.7 | 1.E-02 | 1.8 | S | 3 | |
| Os08g03290.1 | GAPDH | 15 | 2.5 | 6.E-04 | – | X | X | 6 | 1.2 | 4.E-02 | X | X | N/S | |
| Os08g03290.2 | GAPDH | – | X | X | – | X | X | – | X | X | 1.3 | S | N/S | |
| Os03g50480.1 | Phosphoglucomutase | 14 | 6.3 | 2.E-05 | – | X | X | 25 | 2.7 | 2.E-03 | −1.1 | S | N/S | |
| Os02g07260.1 | Phosphoglycerate kinase | 28 | 5.3 | 1.E-04 | – | X | X | 31 | 2.4 | 1.E-02 | 1.2 | S | 2 | |
| Os01g05490.1 | Triosephosphate isomerase | 40 | 2.9 | 5.E-05 | – | X | X | 36 | 1.2 | 9.E-03 | 1.4 | S | 4 and N/S | |
| Os06g13810.1 | PPi-phosphofructokinase | 23 | 2.8 | 2.E-02 | – | X | X | 19 | 2.1 | 9.E-04 | 1.4 | S | 2 | |
| Os05g39310.1 | Pyruvate decarboxylase 1 | – | X | X | – | X | X | – | X | X | 2.0 | S | 594 | |
| Os11g10480.1 | ADH1 | 12 | 6.0 | 2.E-05 | – | X | X | 12 | 3.6 | 4.E-05 | 2.2 | S | 4 | |
| Os01g46070.1 | Malate dehydrogenase | – | X | X | – | X | X | – | X | X | −1.1 | S | N/S | |
| Amino acid synthesis | Os02g50240.1 | Gln synthetase | 38 | −2.3 | 7.E-05 | – | X | X | 34 | −1.3 | 3.E-04 | −2.3 | N/S | −2 |
| Os12g42884.1 | MetSyn | – | X | X | – | X | X | – | X | X | −1.7 | S | −2 and N/S | |
| Os12g42876.1 | MetSyn | 25 | 2.3 | 2.E-03 | – | X | X | 17 | 3.3 | 2.E-03 | −1.7 | S | X | |
| Os12g42876.1 | MetSyn | 26 | 1.1 | 6.E-01 | – | X | X | 18 | 2.7 | 3.E-03 | −1.7 | S | X | |
| Os03g06200.1 | PSAT | 5 | 4.7 | 9.E-07 | 5 | 6.5 | 1.E-03 | – | X | X | 1.7 | N/S | 5 | |
| Os03g06200.1 | PSAT | – | X | X | 9 | 5.6 | 1.E-03 | – | X | X | 1.7 | N/S | 5 | |
| Os12g22030.1 | SHMT | 19 | 1.6 | 9.E-02 | – | X | X | 14 | 2.0 | 4.E-04 | X | X | N/S | |
| Os04g55720.1 | 3-PGDH | 24 | 5.8 | 2.E-05 | – | X | X | 20 | 2.0 | 1.E-03 | 1.9 | S | 4 | |
| Os10g25130.1 | Ala aminotransferase | – | X | X | 15 | 2.5 | 4.E-03 | – | X | X | X | X | N/S | |
| Stress responsive | Os07g44430.1 | Peroxiredoxin | 4 | 5.5 | 6.E-05 | 4 | 11.0 | 5.E-05 | – | X | X | 2.5 | S | 32 |
| Os07g44430.1 | Peroxiredoxin | 3 | 3.4 | 2.E-03 | 3 | 22.7 | 1.E-06 | – | X | X | 2.5 | S | 32 | |
| Os05g25850.1 | Manganese-superoxide dismutase | 1 | 1.6 | 1.E-02 | 1 | 1.9 | 1.E-02 | – | X | X | 1.4 | N/S | N/S | |
| Os03g17690.1 | Ascorbate peroxidase | 39 | −4.6 | 3.E-06 | – | X | X | 13 | −2.3 | 1.E-04 | −1.8 | S | N/S | |
| Os07g49400.1 | Ascorbate peroxidase | – | X | X | – | X | X | – | X | X | −1.9 | S | N/S | |
| Os03g07180.1 | Embryotic protein DC-8 | – | X | X | 10 | 3.5 | 4.E-05 | – | X | X | X | X | X | |
| Os03g07180.1 | Embryotic protein DC-8 | – | X | X | 11 | 3.9 | 3.E-05 | – | X | X | X | X | X | |
| Os03g07180.1 | Embryotic protein DC-8 | – | X | X | 12 | 3.6 | 4.E-05 | – | X | X | X | X | X | |
| Os03g07180.1 | Embryotic protein DC-8 | – | X | X | 13 | 4.7 | 1.E-04 | – | X | X | X | X | X | |
| Os05g46480.1 | LEA group 3 | 2 | 4.1 | 7.E-07 | 2 | 7.1 | 2.E-04 | – | X | X | X | X | −2 | |
| Os02g15250.1 | LEA domain containing | – | X | X | 14 | 5.9 | 8.E-05 | – | X | X | – | X | X | |
| Translation | Os03g14530.1 | S10/S20 ribosomal protein | – | X | X | – | X | X | – | X | X | 1.3 | S | 2 |
| Os11g29190.1 | 40S ribosomal protein S5 | – | X | X | – | X | X | – | X | X | −1.3 | S | 2 | |
| Os03g08010.1 | Elongation factor 1-α | – | X | X | – | X | X | – | X | X | 1.3 | S | N/S | |
| Os01g52470.1 | Elongation factor | – | X | X | – | X | X | – | X | X | 1.4 | S | X | |
| Os02g32030.1 | Elongation factor | – | X | X | – | X | X | – | X | X | −1.1 | S | N/S | |
| Miscellaneous | Os08g04210.1 | Protein kinase | – | X | X | – | X | X | – | X | X | 3.2 | S | 1,007 |
| Os08g04250.1 | Protein kinase | – | X | X | – | X | X | – | X | X | 2.3 | S | 248 | |
| Os08g04240.1 | Protein kinase | – | X | X | – | X | X | – | X | X | 2.8 | S | 525 | |
| Os04g56430.1 | CRK5 | – | X | X | – | X | X | – | X | X | −1.9 | S | 3 | |
| Os01g03340.1 | BBTI4 | 11 | −6.0 | 2.E-06 | – | X | X | – | X | X | −1.9 | S | −3 and −2 | |
| Os01g03360.1 | BBTI5 | – | X | X | – | X | X | – | X | X | 1.1 | S | −2 | |
| Os03g62060.1 | IAA-amino acid hydrolase | 36 | −5.3 | 3.E-04 | 17 | −4.6 | 6.E-03 | 32 | −1.0 | 4.E-01 | −3.0 | S | −271 | |
| Os05g04510.1 | S-Adenosyl-Met synthetase | – | X | X | – | X | X | – | X | X | −1.6 | S | N/S | |